@article {pmid31973163,
year = {2020},
author = {Zhang, GJ and Dong, R and Lan, LN and Li, SF and Gao, WJ and Niu, HX},
title = {Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants.},
journal = {International journal of molecular sciences},
volume = {21},
number = {3},
pages = {},
doi = {10.3390/ijms21030707},
pmid = {31973163},
issn = {1422-0067},
support = {31970240//the National Natural Science foundation of China/ ; },
abstract = {The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.},
}

@article {pmid31972373,
year = {2020},
author = {Muthye, V and Kandoi, G and Lavrov, D},
title = {MMPdb and MitoPredictor: tools for facilitating comparative analysis of animal mitochondrial proteomes.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2020.01.001},
pmid = {31972373},
issn = {1872-8278},
abstract = {Comparative analysis of animal mitochondrial proteomes faces two challenges: the scattering of data on experimentally-characterized animal mitochondrial proteomes across several databases, and the lack of data on mitochondrial proteomes from the majority of metazoan lineages. In this study, we developed two resources to address these challenges: 1] the Metazoan Mitochondrial Proteome Database (MMPdb), which consolidates data on experimentally-characterized mitochondrial proteomes of vertebrate and invertebrate model organisms, and 2] MitoPredictor, a novel machine-learning tool for prediction of mitochondrial proteins in animals. MMPdb allows comparative analysis of animal mitochondrial proteomes by integrating results from orthology analysis, prediction of mitochondrial targeting signals, protein domain analysis, and Gene Ontology analysis. Additionally, for mammalian mitochondrial proteins, MMPdb includes experimental evidence of localization from MitoMiner and the Human Protein Atlas. MMPdb is publicly available at https://mmpdb.eeob.iastate.edu/. MitoPredictor is a Random Forest classifier which uses orthology, mitochondrial targeting signal prediction and protein domain content to predict mitochondrial proteins in animals.},
}

@article {pmid31964548,
year = {2020},
author = {Boos, F and Labbadia, J and Herrmann, JM},
title = {How the Mitoprotein-Induced Stress Response Safeguards the Cytosol: A Unified View.},
journal = {Trends in cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tcb.2019.12.003},
pmid = {31964548},
issn = {1879-3088},
abstract = {Mitochondrial and cytosolic proteostasis are of central relevance for cellular stress resistance and organismal health. Recently, a number of individual cellular programs were described that counter the fatal consequences of mitochondrial dysfunction. These programs remove arrested import intermediates from mitochondrial protein translocases, stabilize protein homeostasis within mitochondria, and, in particular, increase the levels and activity of chaperones and the proteasome system in the cytosol. Here, we describe the different responses to mitochondrial perturbation and propose to unify the seemingly distinct mitochondrial-cytosolic quality control mechanisms into a single network, the mitoprotein-induced stress response. This holistic view places mitochondrial biogenesis at a central position of the cellular proteostasis network, emphasizing the importance of mitochondrial protein import processes for development, reproduction, and ageing.},
}

@article {pmid31963509,
year = {2020},
author = {Toleco, MR and Naake, T and Zhang, Y and Heazlewood, JL and R Fernie, A},
title = {Plant Mitochondrial Carriers: Molecular Gatekeepers That Help to Regulate Plant Central Carbon Metabolism.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/plants9010117},
pmid = {31963509},
issn = {2223-7747},
abstract = {The evolution of membrane-bound organelles among eukaryotes led to a highly compartmentalized metabolism. As a compartment of the central carbon metabolism, mitochondria must be connected to the cytosol by molecular gates that facilitate a myriad of cellular processes. Members of the mitochondrial carrier family function to mediate the transport of metabolites across the impermeable inner mitochondrial membrane and, thus, are potentially crucial for metabolic control and regulation. Here, we focus on members of this family that might impact intracellular central plant carbon metabolism. We summarize and review what is currently known about these transporters from in vitro transport assays and in planta physiological functions, whenever available. From the biochemical and molecular data, we hypothesize how these relevant transporters might play a role in the shuttling of organic acids in the various flux modes of the TCA cycle. Furthermore, we also review relevant mitochondrial carriers that may be vital in mitochondrial oxidative phosphorylation. Lastly, we survey novel experimental approaches that could possibly extend and/or complement the widely accepted proteoliposome reconstitution approach.},
}

@article {pmid31956907,
year = {2020},
author = {Ganesh, S and Horvat, F and Drutovic, D and Efenberkova, M and Pinkas, D and Jindrova, A and Pasulka, J and Iyyappan, R and Malik, R and Susor, A and Vlahovicek, K and Solc, P and Svoboda, P},
title = {The most abundant maternal lncRNA Sirena1 acts post-transcriptionally and impacts mitochondrial distribution.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz1239},
pmid = {31956907},
issn = {1362-4962},
abstract = {Tens of thousands of rapidly evolving long non-coding RNA (lncRNA) genes have been identified, but functions were assigned to relatively few of them. The lncRNA contribution to the mouse oocyte physiology remains unknown. We report the evolutionary history and functional analysis of Sirena1, the most expressed lncRNA and the 10th most abundant poly(A) transcript in mouse oocytes. Sirena1 appeared in the common ancestor of mouse and rat and became engaged in two different post-transcriptional regulations. First, antisense oriented Elob pseudogene insertion into Sirena1 exon 1 is a source of small RNAs targeting Elob mRNA via RNA interference. Second, Sirena1 evolved functional cytoplasmic polyadenylation elements, an unexpected feature borrowed from translation control of specific maternal mRNAs. Sirena1 knock-out does not affect fertility, but causes minor dysregulation of the maternal transcriptome. This includes increased levels of Elob and mitochondrial mRNAs. Mitochondria in Sirena1-/- oocytes disperse from the perinuclear compartment, but do not change in number or ultrastructure. Taken together, Sirena1 contributes to RNA interference and mitochondrial aggregation in mouse oocytes. Sirena1 exemplifies how lncRNAs stochastically engage or even repurpose molecular mechanisms during evolution. Simultaneously, Sirena1 expression levels and unique functional features contrast with the lack of functional importance assessed under laboratory conditions.},
}

@article {pmid31947741,
year = {2020},
author = {Chevigny, N and Schatz-Daas, D and Lotfi, F and Gualberto, JM},
title = {DNA Repair and the Stability of the Plant Mitochondrial Genome.},
journal = {International journal of molecular sciences},
volume = {21},
number = {1},
pages = {},
doi = {10.3390/ijms21010328},
pmid = {31947741},
issn = {1422-0067},
support = {ANR-11-LABX-0057_MITOCROSS//Agence Nationale de la Recherche/ ; },
abstract = {The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.},
}

@article {pmid31936803,
year = {2020},
author = {Wagner, JT and Howe, DK and Estes, S and Denver, DR},
title = {Mitochondrial DNA Variation and Selfish Propagation Following Experimental Bottlenecking in Two Distantly Related Caenorhabditis briggsae Isolates.},
journal = {Genes},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/genes11010077},
pmid = {31936803},
issn = {2073-4425},
support = {GM087628/NH/NIH HHS/United States ; },
abstract = {Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode Caenorhabditis briggsae harbor large, naturally-occurring mtDNA deletions of several hundred basepairs affecting the NADH dehydrogenase subunit 5 (nduo-5) gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which transgenerational mtDNA evolution profiles are shared between isolates that differ in their propensity to accumulate the nduo-5 deletion is also unclear. We address these knowledge gaps by experimentally bottlenecking two isolates of C. briggsae with different nduo-5 deletion frequencies for up to 50 generations and performing total DNA sequencing to identify mtDNA variation. We observed multiple mutation profile differences and similarities between C. briggsae isolates, a potentially species-specific pattern of copy number dysregulation, and some evidence for genetic hitchhiking in the deletion-bearing isolate. Our results further support C. briggsae as a practical model for characterizing naturally-occurring mtgenome variation and contribute to the understanding of how mtgenome variation persists in animal populations and how it presents in mitochondrial disease states.},
}

@article {pmid31233800,
year = {2019},
author = {Bodensohn, US and Simm, S and Fischer, K and Jäschke, M and Groß, LE and Kramer, K and Ehmann, C and Rensing, SA and Ladig, R and Schleiff, E},
title = {The intracellular distribution of the components of the GET system in vascular plants.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {1866},
number = {10},
pages = {1650-1662},
doi = {10.1016/j.bbamcr.2019.06.012},
pmid = {31233800},
issn = {1879-2596},
abstract = {The guided entry of tail-anchored proteins (GET) pathway facilitates targeting and insertion of tail-anchored proteins into membranes. In plants, such a protein insertion machinery for the endoplasmic reticulum as well as constituents within mitochondrial and chloroplasts were discovered. Previous phylogenetic analysis revealed that Get3 sequences of Embryophyta form two clades representing cytosolic ("a") and organellar ("bc") GET3 homologs, respectively. Cellular fractionation of Arabidopsis thaliana seedlings and usage of the self-assembly GFP system in protoplasts verified the cytosolic (ATGet3a), plastidic (ATGet3b) and mitochondrial (ATGet3c) localization of the different homologs. The identified plant homologs of Get1 and Get4 in A. thaliana are localized in ER and cytosol, respectively, implicating a degree of conservation of the GET pathway in A. thaliana. Transient expression of Get3 homologs of Solanum lycopersicum, Medicago × varia or Physcomitrella patens with the self-assembly GFP technique in homologous and heterologous systems verified that multiple Get3 homologs with differing subcellular localizations are common in plants. Chloroplast localized Get3 homologs were detected in all tested plant systems. In contrast, mitochondrial localized Get3 homologs were not identified in S. lycopersicum, or P. patens, while we confirmed on the example of A. thaliana proteins that mitochondrial localized Get3 proteins are properly targeted in S. lycopersicum as well.},
}

@article {pmid31932444,
year = {2020},
author = {Le, T and Žárský, V and Nývltová, E and Rada, P and Harant, K and Vancová, M and Verner, Z and Hrdý, I and Tachezy, J},
title = {Anaerobic peroxisomes in Mastigamoeba balamuthi.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1909755117},
pmid = {31932444},
issn = {1091-6490},
abstract = {The adaptation of eukaryotic cells to anaerobic conditions is reflected by substantial changes to mitochondrial metabolism and functional reduction. Hydrogenosomes belong among the most modified mitochondrial derivative and generate molecular hydrogen concomitant with ATP synthesis. The reduction of mitochondria is frequently associated with loss of peroxisomes, which compartmentalize pathways that generate reactive oxygen species (ROS) and thus protect against cellular damage. The biogenesis and function of peroxisomes are tightly coupled with mitochondria. These organelles share fission machinery components, oxidative metabolism pathways, ROS scavenging activities, and some metabolites. The loss of peroxisomes in eukaryotes with reduced mitochondria is thus not unexpected. Surprisingly, we identified peroxisomes in the anaerobic, hydrogenosome-bearing protist Mastigamoeba balamuthi We found a conserved set of peroxin (Pex) proteins that are required for protein import, peroxisomal growth, and division. Key membrane-associated Pexs (MbPex3, MbPex11, and MbPex14) were visualized in numerous vesicles distinct from hydrogenosomes, the endoplasmic reticulum (ER), and Golgi complex. Proteomic analysis of cellular fractions and prediction of peroxisomal targeting signals (PTS1/PTS2) identified 51 putative peroxisomal matrix proteins. Expression of selected proteins in Saccharomyces cerevisiae revealed specific targeting to peroxisomes. The matrix proteins identified included components of acyl-CoA and carbohydrate metabolism and pyrimidine and CoA biosynthesis, whereas no components related to either β-oxidation or catalase were present. In conclusion, we identified a subclass of peroxisomes, named "anaerobic" peroxisomes that shift the current paradigm and turn attention to the reductive evolution of peroxisomes in anaerobic organisms.},
}

@article {pmid31610813,
year = {2019},
author = {Motoki, MT and Fonseca, DM and Miot, EF and Demari-Silva, B and Thammavong, P and Chonephetsarath, S and Phommavanh, N and Hertz, JC and Kittayapong, P and Brey, PT and Marcombe, S},
title = {Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People's Democratic Republic.},
journal = {Parasites & vectors},
volume = {12},
number = {1},
pages = {477},
pmid = {31610813},
issn = {1756-3305},
mesh = {Aedes/classification/genetics/*physiology/virology ; Algorithms ; Animals ; Asia, Southeastern ; Bayes Theorem ; Cluster Analysis ; DNA/chemistry/isolation & purification ; Electron Transport Complex IV/genetics ; Far East ; Female ; Genetic Variation ; Genetics, Population ; Haplotypes ; Italy ; Laos ; Mitochondria/enzymology ; Mosquito Control ; Mosquito Vectors/classification/genetics/*physiology/virology ; Phylogeny ; Sequence Analysis, DNA ; Tropical Climate ; United States ; },
abstract = {BACKGROUND: The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR.

METHODS: We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA.

RESULTS: We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions.

CONCLUSIONS: Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.},
}

Aedes/classification/genetics/*physiology/virology
Algorithms
Animals
Asia, Southeastern
Bayes Theorem
Cluster Analysis
DNA/chemistry/isolation & purification
Electron Transport Complex IV/genetics
Far East
Female
Genetic Variation
Genetics, Population
Haplotypes
Italy
Laos
Mitochondria/enzymology
Mosquito Control
Mosquito Vectors/classification/genetics/*physiology/virology
Phylogeny
Sequence Analysis, DNA
Tropical Climate
United States

@article {pmid31928187,
year = {2020},
author = {Jastroch, M and Seebacher, F},
title = {Importance of adipocyte browning in the evolution of endothermy.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1793},
pages = {20190134},
doi = {10.1098/rstb.2019.0134},
pmid = {31928187},
issn = {1471-2970},
abstract = {Endothermy changes the relationship between organisms and their environment fundamentally, and it is therefore of major ecological and evolutionary significance. Endothermy is characterized by non-shivering thermogenesis, that is metabolic heat production in the absence of muscular activity. In many eutherian mammals, brown adipose tissue (BAT) is an evolutionary innovation that facilitates non-shivering heat production in mitochondria by uncoupling food-derived substrate oxidation from chemical energy (ATP) production. Consequently, energy turnover is accelerated resulting in increased heat release. The defining characteristics of BAT are high contents of mitochondria and vascularization, and the presence of uncoupling protein 1. Recent insights, however, reveal that a range of stimuli such as exercise, diet and the immune system can cause the browning of white adipocytes, thereby increasing energy expenditure and heat production even in the absence of BAT. Here, we review the molecular mechanisms that cause browning of white adipose tissue, and their potential contribution to thermoregulation. The significance for palaeophysiology lies in the presence of adipose tissue and the mechanisms that cause its browning and uncoupling in all amniotes. Hence, adipocytes may have played a role in the evolution of endothermy beyond the more specific evolution of BAT in eutherians. This article is part of the theme issue 'Vertebrate palaeophysiology'.},
}

@article {pmid31203477,
year = {2019},
author = {Hu, F and Fan, J and Wu, C and Zhu, M and Zhou, Y and Wang, S and Zhang, C and Tao, M and Zhao, R and Tang, C and Luo, K and Qin, Q and Ma, M and Chen, B and Wang, J and Zhou, A and Bai, L and Liu, S},
title = {Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {21},
number = {4},
pages = {515-525},
doi = {10.1007/s10126-019-09899-6},
pmid = {31203477},
issn = {1436-2236},
support = {31802286//National Natural Science Foundation of China/International ; 31430088//National Natural Science Foundation of China/International ; 31730098//National Natural Science Foundation of China/International ; 2018M642986//Postdoctoral Research Foundation of China/International ; CARS-45//Earmarked Fund for China Agriculture Research System/International ; },
mesh = {Animals ; Chromosomes/*chemistry ; Cyprinidae/classification/*genetics ; Gene Ontology ; *Genome ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Karyotype ; Mitochondria/genetics ; Molecular Sequence Annotation ; Phylogeny ; Ploidies ; Sequence Analysis, DNA ; *Transcriptome ; },
abstract = {Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-length transcriptome of O. brevibarba derived from 5 different tissues using the PacBio SMRT sequencing. The result shows that O. brevibarba was a diploid with 50 chromosomes [corrected]. The complete mitogenome of O. brevibarba was 16,602 bp in size and very similar (89.1-91.3%) to that of other Onychostoma species but was distinct from all congeners. The full-length transcriptome dataset of O. brevibarba comprised 120,239 unigenes. Among the unigenes, 91,542 were functionally annotated, whereas 26,794 were found to have two or more isoforms. This study could provide many new insights into cytology and molecular characteristics of O. brevibarba; it laid the foundation for further exploration of the genomic signatures of species of Onychostoma.},
}

Animals
Chromosomes/*chemistry
Cyprinidae/classification/*genetics
Gene Ontology
*Genome
*Genome, Mitochondrial
High-Throughput Nucleotide Sequencing
Karyotype
Mitochondria/genetics
Molecular Sequence Annotation
Phylogeny
Ploidies
Sequence Analysis, DNA
*Transcriptome

@article {pmid31915815,
year = {2020},
author = {Zumkeller, S and Gerke, P and Knoop, V},
title = {A functional twintron, 'zombie' twintrons and a hypermobile group II intron invading itself in plant mitochondria.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz1194},
pmid = {31915815},
issn = {1362-4962},
abstract = {The occurrence of group II introns in plant mitochondrial genomes is strikingly different between the six major land plant clades, contrasting their highly conserved counterparts in chloroplast DNA. Their present distribution likely reflects numerous ancient intron gains and losses during early plant evolution before the emergence of seed plants. As a novelty for plant organelles, we here report on five cases of twintrons, introns-within-introns, in the mitogenomes of lycophytes and hornworts. An internal group II intron interrupts an intron-borne maturase of an atp9 intron in Lycopodiaceae, whose splicing precedes splicing of the external intron. An invasive, hypermobile group II intron in cox1, has conquered nine further locations including a previously overlooked sdh3 intron and, most surprisingly, also itself. In those cases, splicing of the external introns does not depend on splicing of the internal introns. Similar cases are identified in the mtDNAs of hornworts. Although disrupting a group I intron-encoded protein in one case, we could not detect splicing of the internal group II intron in this 'mixed' group I/II twintron. We suggest the name 'zombie' twintrons (half-dead, half-alive) for such cases where splicing of external introns does not depend any more on prior splicing of fossilized internal introns.},
}

@article {pmid31915577,
year = {2020},
author = {Repetti, SI and Jackson, CJ and Judd, LM and Wick, RR and Holt, KE and Verbruggen, H},
title = {The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8273},
doi = {10.7717/peerj.8273},
pmid = {31915577},
issn = {2167-8359},
abstract = {Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.},
}

@article {pmid31042716,
year = {2019},
author = {Tiukova, IA and Pettersson, ME and Hoeppner, MP and Olsen, RA and Käller, M and Nielsen, J and Dainat, J and Lantz, H and Söderberg, J and Passoth, V},
title = {Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0215077},
doi = {10.1371/journal.pone.0215077},
pmid = {31042716},
issn = {1932-6203},
mesh = {Brettanomyces/genetics/*metabolism ; Chromosomes, Fungal/*genetics ; Contig Mapping ; Ethanol/*metabolism ; Evolution, Molecular ; Gene Dosage ; Genetic Variation ; Genome Size ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Whole Genome Sequencing/methods ; },
abstract = {Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.},
}

Brettanomyces/genetics/*metabolism
Chromosomes, Fungal/*genetics
Contig Mapping
Ethanol/*metabolism
Evolution, Molecular
Gene Dosage
Genetic Variation
Genome Size
Mitochondria/*genetics
Molecular Sequence Annotation
Phylogeny
Whole Genome Sequencing/methods

@article {pmid31018611,
year = {2019},
author = {Crottini, A and Orozco-terWengel, P and Rabemananjara, FCE and Hauswaldt, JS and Vences, M},
title = {Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella.},
journal = {Genes},
volume = {10},
number = {4},
pages = {},
doi = {10.3390/genes10040317},
pmid = {31018611},
issn = {2073-4425},
mesh = {Animals ; Anura/*classification/genetics ; Biodiversity ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Introgression ; Genetics, Population ; Homeodomain Proteins/genetics ; Madagascar ; Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; Skin Pigmentation/*genetics ; },
abstract = {Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantellamadagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantellaaurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantellacrocea + Mantellamilotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes.},
}

Animals
Anura/*classification/genetics
Biodiversity
DNA, Mitochondrial/genetics
Gene Flow
Genetic Introgression
Genetics, Population
Homeodomain Proteins/genetics
Madagascar
Microsatellite Repeats
Mitochondria/*genetics
Phylogeny
Sequence Analysis, DNA/*veterinary
Skin Pigmentation/*genetics

@article {pmid31242450,
year = {2019},
author = {Roy, P and Rout, AK and Maharana, J and Sahoo, DR and Panda, SP and Pal, A and Nayak, KK and Behera, BK and Das, BK},
title = {Molecular characterization, constitutive expression and GTP binding mechanism of Cirrhinus mrigala (Hamilton, 1822) Myxovirus resistance (Mx) protein.},
journal = {International journal of biological macromolecules},
volume = {136},
number = {},
pages = {1258-1272},
doi = {10.1016/j.ijbiomac.2019.06.161},
pmid = {31242450},
issn = {1879-0003},
mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cypriniformes/*genetics ; DNA, Complementary/genetics ; Fish Proteins/chemistry/*genetics/*metabolism ; *Gene Expression Regulation ; Guanosine Triphosphate/*metabolism ; Kinetics ; Molecular Dynamics Simulation ; Myxovirus Resistance Proteins/chemistry/*genetics/*metabolism ; Phylogeny ; Protein Binding ; Protein Domains ; Protein Stability ; RNA, Messenger/genetics ; Thermodynamics ; },
abstract = {Myxovirus resistance (Mx) proteins represents the subclass of the dynamin superfamily of large Guanosine triphosphates (GTPases), play esential role in intracellular vesicle trafficking, endocytosis, organelle homeostasis and mitochondria distribution. These proteins are key players of the vertebrate immune system, induced by type-I and type-III interferons (IFN) of infected host and inhibit viral replication by sequestering its nucleoprotein. In the present study, we report the sequencing and characterization of Cirrhinus mrigala Mx protein (CmMx) for the first time and observed its constitutive expression in different tissues for a period of fourteen days. The synthetic peptide, LSGVALPRGTGI, was dissolved in PBS and injected into a rabbit and the antibody raised against CmMx was used to study the level of its expression. The full length of the CmMx cDNA is 2244 bp with a molecular mass of 70.9 kDa and a predicted isoelectric point of 8.25. The 627 amino acids polypeptide formed of three main functional domains: N-terminal GTPase domain (GD), a middle domain (MD) and GTPase effector domain (GED) with carboxy terminal leucine zipper motif. The 3D models of CmMx protein was modeled based on available close structural homologs and further validated through molecular dynamics (MD) simulations. MD study revealed the importance of G-domain responsible for recognition of GTP, which perfectly corroborate with earlier studies. MM/PBSA binding free energy analysis displayed that van der Waals and electrostatic energy were the key driving force behind molecular recognition of GTP by CmMx protein. The results from this study will illuminate more lights into the ongoing research on myxovirus resistance protein and its role in inhibition of viral replication in other eukaryotic system as well.},
}

Amino Acid Sequence
Animals
Cloning, Molecular
Cypriniformes/*genetics
DNA, Complementary/genetics
Fish Proteins/chemistry/*genetics/*metabolism
*Gene Expression Regulation
Guanosine Triphosphate/*metabolism
Kinetics
Molecular Dynamics Simulation
Myxovirus Resistance Proteins/chemistry/*genetics/*metabolism
Phylogeny
Protein Binding
Protein Domains
Protein Stability
RNA, Messenger/genetics
Thermodynamics

@article {pmid31125665,
year = {2019},
author = {Liu, W and Chen, B and Chen Li, and Yao, J and Liu, J and Kuang, M and Wang, F and Wang, Y and Elkady, G and Lu, Y and Zhang, Y and Liu, X},
title = {Identification of fish CMPK2 as an interferon stimulated gene against SVCV infection.},
journal = {Fish & shellfish immunology},
volume = {92},
number = {},
pages = {125-132},
doi = {10.1016/j.fsi.2019.05.032},
pmid = {31125665},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Fish Diseases/*immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation/*immunology ; Immunity, Innate/*genetics ; Interferons/metabolism ; Phylogeny ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology/veterinary ; Sequence Alignment/veterinary ; Zebrafish/*genetics/*immunology ; },
abstract = {Cytidine/uridine monophosphate kinase 2 (CMPK2) is known as a nucleoside monophosphate kinase in mitochondria to maintains intracellular UTP/CTP, and could be induced by immunostimulants LPS and Poly (I:C) in mammals, suggesting its potential antiviral and antibacterial role. In this study, CMPK2 was cloned and characterized in Fathead minnow (FHM) cells. In vivo analysis of tissue distribution revealed that CMPK2 transcript was detected in all the tissues of zebrafish (Danio rerio) examined in this study, particularly abundant in liver, spleen and kidney. In addition, indirect immunofluorescence showed that CMPK2 was localized in the cytoplasm of FHM cells. Expression of CMPK2 mRNA was significantly up-regulated following challenge with Spring viraemia of carp virus (SVCV), poly(I:C), or zebrafish IFN1 and IFN3 both in vitro and in vivo. Furthermore, overexpression and RNA interference of CMPK2 in SVCV-infected FHM cells showed significantly antiviral effect. In summary, this study for the first time shows the presence and distribution of CMPK2 in different tissues of zebrafish, but also demonstrates its antiviral potential against SVCV infection in vivo. These new findings could contribute to explain the molecular mechanism of the CMPK2 mediated antiviral function.},
}

Amino Acid Sequence
Animals
Fish Diseases/*immunology
Gene Expression Profiling/veterinary
Gene Expression Regulation/*immunology
Immunity, Innate/*genetics
Interferons/metabolism
Phylogeny
Rhabdoviridae/physiology
Rhabdoviridae Infections/immunology/veterinary
Sequence Alignment/veterinary
Zebrafish/*genetics/*immunology

@article {pmid31673867,
year = {2019},
author = {Puri, RR and Adachi, F and Omichi, M and Saeki, Y and Yamamoto, A and Hayashi, S and Ali, MA and Itoh, K},
title = {Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions.},
journal = {World journal of microbiology & biotechnology},
volume = {35},
number = {11},
pages = {176},
pmid = {31673867},
issn = {1573-0972},
support = {16KT0032//Japan Society for the Promotion of Science/ ; },
mesh = {Bacteria/*classification/genetics/*metabolism ; Base Sequence ; Biodiversity ; *Climate ; DNA, Bacterial/analysis ; DNA, Mitochondrial/analysis ; Endophytes/*classification/genetics ; Ipomoea batatas/*microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.},
}

Bacteria/*classification/genetics/*metabolism
Base Sequence
Biodiversity
*Climate
DNA, Bacterial/analysis
DNA, Mitochondrial/analysis
Endophytes/*classification/genetics
Ipomoea batatas/*microbiology
*Metagenome
*Microbiota/genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Soil/*chemistry
Soil Microbiology

@article {pmid30508570,
year = {2019},
author = {Hiltunen, JK and Kastaniotis, AJ and Autio, KJ and Jiang, G and Chen, Z and Glumoff, T},
title = {17B-hydroxysteroid dehydrogenases as acyl thioester metabolizing enzymes.},
journal = {Molecular and cellular endocrinology},
volume = {489},
number = {},
pages = {107-118},
doi = {10.1016/j.mce.2018.11.012},
pmid = {30508570},
issn = {1872-8057},
mesh = {17-Hydroxysteroid Dehydrogenases/chemistry/*metabolism ; Animals ; Disease ; Esters/*metabolism ; Fatty Acids, Unsaturated/metabolism ; Humans ; Mitochondria/metabolism ; RNA/metabolism ; },
abstract = {17β-Hydroxysteroid dehydrogenases (HSD17B) catalyze the oxidation/reduction of 17β-hydroxy/keto group in position C17 in C18- and C19 steroids. Most HSD17Bs are also catalytically active with substrates other than steroids. A subset of these enzymes is able to process thioesters of carboxylic acids. This group of enzymes includes HSD17B4, HSD17B8, HSD17B10 and HSD17B12, which execute reactions in intermediary metabolism, participating in peroxisomal β-oxidation of fatty acids, mitochondrial oxidation of 3R-hydroxyacyl-groups, breakdown of isoleucine and fatty acid chain elongation in endoplasmic reticulum. Divergent substrate acceptance capabilities exemplify acquirement of catalytic site adaptiveness during evolution. As an additional common feature these HSD17Bs are multifunctional enzymes that arose either via gene fusions (HSD17B4) or are incorporated as subunits into multifunctional protein complexes (HSD17B8 and HSD17B10). Crystal structures of HSD17B4, HSD17B8 and HSD17B10 give insight into their structure-function relationships. Thus far, deficiencies of HSD17B4 and HSD17B10 have been assigned to inborn errors in humans, underlining their significance as enzymes of metabolism.},
}

17-Hydroxysteroid Dehydrogenases/chemistry/*metabolism
Animals
Disease
Esters/*metabolism
Fatty Acids, Unsaturated/metabolism
Humans
Mitochondria/metabolism
RNA/metabolism

@article {pmid31901107,
year = {2020},
author = {Yoneva, A and Kuchta, R and Smit, N},
title = {Ultrastructure of the uterus, embryonic envelopes and the coracidium of the enigmatic tapeworm Tetracampos ciliotheca (Cestoda: Bothriocephalidea) from African sharptooth catfish (Clarias gariepinus).},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00436-019-06496-3},
pmid = {31901107},
issn = {1432-1955},
abstract = {Transmission electron microscopy (TEM) was used to study the ultrastructure of the uterus and egg morphology in the enigmatic bothriocephalidean tapeworm Tetracampos ciliotheca. The uterine wall, underlain by well-developed muscle bundles, consists of a syncytial epithelium which is characterized by the abundance of free ribosomes, mitochondria and cisternae of granular endoplasmic reticulum (GER). On the apical surface of the uterine epithelium, there is an abundant network of cytoplasmic microlamellae projecting into the uterine lumen. The lumen is filled with freely lying eggs which are located close to the uterine wall but do not contact with the microlamellae of the uterine epithelium. The developed eggs possess an oncosphere surrounded by four envelopes: (1) a thin egg shell; (2) an outer envelope; (3) a syncytial, ciliated inner envelope; and (4) the oncospheral membrane. The mature hexacanth is armed with three pairs of oncospheral hooks, as well as somatic and hook muscles and five types of cells (1) binucleated subtegumental cell, (2) somatic cells, (3) penetration gland cells, (4) nerve cells and (5) germinative cells. Considering the relative scarcity of descriptive and comparative studies on the ultrastructure of the uterus and egg morphology in the order Bothriocephalidea, we concluded that Tet. ciliotheca displays a unique type of egg development. Based on these results, we discuss plausible ideas relating to the function of these structures for consideration in future studies.},
}

@article {pmid31534121,
year = {2019},
author = {Marques, DA and Lucek, K and Sousa, VC and Excoffier, L and Seehausen, O},
title = {Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4240},
doi = {10.1038/s41467-019-12182-w},
pmid = {31534121},
issn = {2041-1723},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Gene Flow ; *Genetic Speciation ; Genetics, Population ; Genome/genetics ; Lakes ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Polymorphism, Single Nucleotide/genetics ; Rivers ; Smegmamorpha/*classification/*genetics ; Sympatry/*genetics ; },
abstract = {Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation.},
}

Animals
DNA, Mitochondrial/genetics
Gene Flow
*Genetic Speciation
Genetics, Population
Genome/genetics
Lakes
Microsatellite Repeats/genetics
Mitochondria/genetics
Polymorphism, Single Nucleotide/genetics
Rivers
Smegmamorpha/*classification/*genetics
Sympatry/*genetics

@article {pmid31894631,
year = {2020},
author = {Ghemari, C and Jelassi, R and Khemaissia, H and Waterlot, C and Raimond, M and Souty-Grosset, C and Douay, F and Nasri-Ammar, K},
title = {Physiological and histopathological responses of Porcellio laevis (Isopoda, Crustacea) as indicators of metal trace element contamination.},
journal = {Microscopy research and technique},
volume = {},
number = {},
pages = {},
doi = {10.1002/jemt.23428},
pmid = {31894631},
issn = {1097-0029},
abstract = {This study was designed to assess the impact of the mixture of cadmium (Cd) and zinc (Zn) on the bioaccumulation and the ultrastructural changes in the hepatopancreas of Porcellio laevis (Latreille, 1804) after 4 weeks of exposure to contaminated Quercus leaves under laboratory conditions. For each metal, four concentrations were used with four replicates for each concentration. Metal concentrations in the hepatopancreas and the rest of the body were determined using atomic absorption spectrometry. From the first week until the end of the experiment, a weight gain in P. laevis was observed particularly between the first and the end of exposure from 93.3 ± 18.22 mg fw to 105.22 ± 16.16 mg fw and from 106.4 ± 22.67 mg fw to 125.9 ± 23.9 mg fw for Mix1 and Mix4, respectively. Additionally, the determined metal trace elements (MTE) concentrations in the hepatopancreas were considerably higher compared to those in the rest of the body and seem to be dose-dependent. Using transmission electron microscopy (TEM), some alterations were highlighted in the hepatopancreas. The main observed alterations were (a) the destruction of the microvilli border in a considerable portion of cells, (b) the increase of the lipid droplets with different shapes and sizes, (c) the increase in the number of the mitochondria, and (d) the appearance of TE in the form of B-type granules. The obtained results confirmed the ability of P. laevis to deal with high amounts of MTE, suggesting its possible use in future soil's biomonitoring programs.},
}

@article {pmid31888949,
year = {2019},
author = {Sun, S and Fu, C and Ianiri, G and Heitman, J},
title = {The Pheromone and Pheromone Receptor Mating-Type Locus Is Involved in Controlling Uniparental Mitochondrial Inheritance in Cryptococcus.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1534/genetics.119.302824},
pmid = {31888949},
issn = {1943-2631},
abstract = {Mitochondria are inherited uniparentally during sexual reproduction in the majority of eukaryotic species studied, including humans, mice, nematodes, as well as many fungal species. Mitochondrial uniparental inheritance (mito-UPI) could be beneficial in that it avoids possible genetic conflicts between organelles with different genetic backgrounds, as recently shown in mice; and it could prevent the spread of selfish genetic elements in the mitochondrial genome. Despite the prevalence of observed mito-UPI, the underlying mechanisms and the genes involved in controlling this non-mendelian inheritance are poorly understood in many species. In Cryptococcus neoformans, a human pathogenic basidiomyceteous fungus, mating types (MATα and MATa) are defined by alternate alleles at the single MAT locus that evolved from fusion of the two MAT loci (P/R encoding pheromones and pheromone receptors, HD encoding homeodomain transcription factors) that are the ancestral state in the basidiomycota. Mitochondria are inherited uniparentally from the MATa parent in C. neoformans and this requires the SXI1α and SXI2a HD factors encoded by MAT However, there is evidence additional genes contribute to control of mito-UPI in Cryptococcus Here we show that in Cryptococcus amylolentus, a sibling species of C. neoformans with unlinked P/R and HDMAT loci, mitochondrial uniparental inheritance is controlled by the P/R locus, and is independent of the HD locus. Consistently, by replacing the MATα alleles of the pheromones (MF) and pheromone receptor (STE3) with the MATa alleles, we show that these P/R locus defining genes indeed affect mito-UPI in C. neoformans during sexual reproduction. Additionally, we show that during early stages of C. neoformans sexual reproduction, conjugation tubes are always produced by the MATα cells, resulting in unidirectional migration of the MATα nucleus into the MATa cell during zygote formation. This process is controlled by the P/R locus and could serve to physically restrict movement of MATα mitochondria in the zygotes, and thereby contribute to mito-UPI. We propose a model in which both physical and genetic mechanisms function in concert to prevent the coexistence of mitochondria from the two parents in the zygote and subsequently in the meiotic progeny, thus ensuring mito-UPI in pathogenic Cryptococcus, as well as in closely related non-pathogenic species. The implications of these findings are discussed in the context of the evolution of mito-UPI in fungi and other more diverse eukaryotes.},
}

@article {pmid31883789,
year = {2019},
author = {Namba, T and Dóczi, J and Pinson, A and Xing, L and Kalebic, N and Wilsch-Bräuninger, M and Long, KR and Vaid, S and Lauer, J and Bogdanova, A and Borgonovo, B and Shevchenko, A and Keller, P and Drechsel, D and Kurzchalia, T and Wimberger, P and Chinopoulos, C and Huttner, WB},
title = {Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuron.2019.11.027},
pmid = {31883789},
issn = {1097-4199},
abstract = {The human-specific gene ARHGAP11B is preferentially expressed in neural progenitors of fetal human neocortex and increases abundance and proliferation of basal progenitors (BPs), which have a key role in neocortex expansion. ARHGAP11B has therefore been implicated in the evolutionary expansion of the human neocortex, but its mode of action has been unknown. Here, we show that ARHGAP11B is imported into mitochondria, where it interacts with the adenine nucleotide translocase (ANT) and inhibits the mitochondrial permeability transition pore (mPTP). BP expansion by ARHGAP11B requires its presence in mitochondria, and pharmacological inhibition of ANT function or mPTP opening mimic BP expansion by ARHGAP11B. Searching for the underlying metabolic basis, we find that BP expansion by ARHGAP11B requires glutaminolysis, the conversion of glutamine to glutamate for the tricarboxylic acid (TCA) cycle. Hence, an ARHGAP11B-induced, mitochondria-based effect on BP metabolism that is a hallmark of highly mitotically active cells appears to underlie its role in neocortex expansion.},
}

@article {pmid31881590,
year = {2012},
author = {Lagaudrière-Gesbert, C and Purvina, M and Assrir, N and Rossignol, JM},
title = {Rôle(s) de la protéine cellulaire gC1qR dans les cycles viraux.},
journal = {Virologie (Montrouge, France)},
volume = {16},
number = {2},
pages = {85-94},
doi = {10.1684/vir.2012.0443},
pmid = {31881590},
issn = {1267-8694},
abstract = {The cellular protein gC1qR (also named HABP1, p32, p33 or TAP) has been identified as a partner of several viral proteins belonging to different virus families. gC1qR is a mitochondrial protein also present at the cell surface and in the nucleus. In normal cells, gC1qR seems involved in diverse biological processes related to its cellular localization. gC1qR could be involved in apoptosis in mitochondria, in RNA splicing in the nucleus or in immune and inflammatory responses at the cell surface. The multiple functions of gC1qR, as the variety of its viral partners, raise the question of its possible function(s) in the viral cycle. The goal of this review is to: (i) summarize what is known about gC1qR, (ii) focus on the demonstrated or hypothetical functions of the gC1qR-viral proteins complexes reported in the literature and (iii) propose a model on the possible roles of gC1qR in the viral life cycles.},
}

@article {pmid31575774,
year = {2019},
author = {Murante, D and Hogan, DA},
title = {New Mitochondrial Targets in Fungal Pathogens.},
journal = {mBio},
volume = {10},
number = {5},
pages = {},
pmid = {31575774},
issn = {2150-7511},
mesh = {*Candida albicans ; Humans ; *Mitochondria ; Phylogeny ; Saccharomyces cerevisiae ; },
abstract = {In eukaryotic cells, mitochondria are responsible for the synthesis of ATP using power generated by the electron transport chain (ETC). While much of what is known about mitochondria has been gained from a study of a small number of model species, including the yeast Saccharomyces cerevisiae, the general mechanisms of mitochondrial respiration have been recognized as being highly conserved across eukaryotes. Now, Sun et al. (N. Sun, R. S. Parrish, R. A. Calderone, and W. A. Fonzi, mBio 10:e00300-19, 2019, https://doi.org/10.1128/mBio.00300-19) take the next steps in understanding mitochondrial function by identifying proteins that are unique to a smaller phylogenetic group of microbes. Using the combination of in silico, biochemical, and microbiological assays, Sun and colleagues identified seven genes that are unique to the CTG fungal clade, which contains multiple important human pathogens, including Candida albicans, and showed that they are required for full ETC function during respiratory metabolism. Because respiratory metabolism is critical for fungal pathogenesis, these clade-specific mitochondrial factors may represent novel therapeutic targets.},
}

*Candida albicans
Humans
*Mitochondria
Phylogeny
Saccharomyces cerevisiae

@article {pmid31881218,
year = {2019},
author = {Ji, SG and Medvedeva, YV and Weiss, JH},
title = {Zn2+ entry through the mitochondrial calcium uniporter is a critical contributor to mitochondrial dysfunction and neurodegeneration.},
journal = {Experimental neurology},
volume = {},
number = {},
pages = {113161},
doi = {10.1016/j.expneurol.2019.113161},
pmid = {31881218},
issn = {1090-2430},
abstract = {Excitotoxic Ca2+ accumulation contributes to ischemic neurodegeneration, and Ca2+ can enter the mitochondria through the mitochondrial calcium uniporter (MCU) to promote mitochondrial dysfunction. Yet, Ca2+-targeted therapies have met limited success. A growing body of evidence has highlighted the underappreciated importance of Zn2+, which also accumulates in neurons after ischemia and can induce mitochondrial dysfunction and cell death. While studies have indicated that Zn2+ can also enter the mitochondria through the MCU, the specificity of the pore's role in Zn2+-triggered injury is still debated. Present studies use recently available MCU knockout mice to examine how the deletion of this channel impacts deleterious effects of cytosolic Zn2+ loading. In cultured cortical neurons from MCU knockout mice, we find significantly reduced mitochondrial Zn2+ accumulation. Correspondingly, these neurons were protected from both acute and delayed Zn2+-triggered mitochondrial dysfunction, including mitochondrial reactive oxygen species generation, depolarization, swelling and inhibition of respiration. Furthermore, when toxic extramitochondrial effects of Ca2+ entry were moderated, both cultured neurons (exposed to Zn2+) and CA1 neurons of hippocampal slices (subjected to prolonged oxygen glucose deprivation to model ischemia) from MCU knockout mice displayed decreased neurodegeneration. Finally, to examine the therapeutic applicability of these findings, we added an MCU blocker after toxic Zn2+ exposure in wildtype neurons (to induce post-insult MCU blockade). This significantly attenuated the delayed evolution of both mitochondrial dysfunction and neurotoxicity. These data-combining both genetic and pharmacologic tools-support the hypothesis that Zn2+ entry through the MCU is a critical contributor to ischemic neurodegeneration that could be targeted for neuroprotection.},
}

@article {pmid30841657,
year = {2019},
author = {Yang, T and Xu, G and Gu, B and Shi, Y and Mzuka, HL and Shen, H},
title = {The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis.},
journal = {Genes},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/genes10030198},
pmid = {30841657},
issn = {2073-4425},
mesh = {Amino Acid Sequence ; Animals ; Gastropoda/*classification/genetics ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Whole Genome Sequencing/*methods ; },
abstract = {The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.},
}

Amino Acid Sequence
Animals
Gastropoda/*classification/genetics
Genome Size
Genome, Mitochondrial
Mitochondria/*genetics
Phylogeny
Whole Genome Sequencing/*methods

@article {pmid31035578,
year = {2019},
author = {Banguera-Hinestroza, E and Ferrada, E and Sawall, Y and Flot, JF},
title = {Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments.},
journal = {Genes},
volume = {10},
number = {5},
pages = {},
doi = {10.3390/genes10050324},
pmid = {31035578},
issn = {2073-4425},
mesh = {Animals ; Anthozoa/*genetics ; *Computational Biology ; DNA, Mitochondrial/*genetics ; Ecosystem ; Indian Ocean ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Phylogeography ; Protein Conformation ; Tandem Repeat Sequences/genetics ; },
abstract = {More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.},
}

Animals
Anthozoa/*genetics
*Computational Biology
DNA, Mitochondrial/*genetics
Ecosystem
Indian Ocean
Mitochondria/*genetics
Open Reading Frames/genetics
Phylogeny
Phylogeography
Protein Conformation
Tandem Repeat Sequences/genetics

@article {pmid31873127,
year = {2019},
author = {Terrien, J and Seugnet, I and Seffou, B and Herrero, MJ and Bowers, J and Chamas, L and Decherf, S and Duvernois-Berthet, E and Djediat, C and Ducos, B and Demeneix, BA and Clerget-Froidevaux, MS},
title = {Reduced central and peripheral inflammatory responses and increased mitochondrial activity contribute to diet-induced obesity resistance in WSB/EiJ mice.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {19696},
doi = {10.1038/s41598-019-56051-4},
pmid = {31873127},
issn = {2045-2322},
support = {GA-259772//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-602757//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-259772//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-602757//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-238665//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-259772//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-602757//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-259772//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-602757//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-259772//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-602757//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-259772//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; GA-602757//EC | EC Seventh Framework Programm | FP7 Health (FP7-HEALTH - Specific Programme "Cooperation": Health)/ ; },
abstract = {Energy imbalance due to excess of calories is considered to be a major player in the current worldwide obesity pandemic and could be accompanied by systemic and central inflammation and mitochondrial dysfunctions. This hypothesis was tested by comparing the wild-derived diet-induced obesity- (DIO-) resistant mouse strain WSB/EiJ to the obesity-prone C57BL/6J strain. We analysed circulating and hypothalamic markers of inflammatory status and hypothalamic mitochondrial activity in both strains exposed to high-fat diet (HFD). We further analysed the regulations of hypothalamic genes involved in inflammation and mitochondrial pathways by high throughput microfluidic qPCR on RNA extracted from laser micro-dissected arcuate (ARC) and paraventricular (PVN) hypothalamic nuclei. HFD induced increased body weight gain, circulating levels of leptin, cholesterol, HDL and LDL in C57BL/6J whereas WSB/EiJ mice displayed a lower inflammatory status, both peripherally (lower levels of circulating cytokines) and centrally (less activated microglia in the hypothalamus) as well as more reactive mitochondria in the hypothalamus. The gene expression data analysis allowed identifying strain-specific hypothalamic metabolic pathways involved in the respective responses to HFD. Our results point to the involvement of hypothalamic inflammatory and mitochondrial pathways as key factors in the control of energy homeostasis and the resistance to DIO.},
}

@article {pmid31211668,
year = {2019},
author = {Nascimento, FS and Barta, JR and Whale, J and Hofstetter, JN and Casillas, S and Barratt, J and Talundzic, E and Arrowood, MJ and Qvarnstrom, Y},
title = {Mitochondrial Junction Region as Genotyping Marker for Cyclospora cayetanensis.},
journal = {Emerging infectious diseases},
volume = {25},
number = {7},
pages = {1314-1319},
doi = {10.3201/eid2507.181447},
pmid = {31211668},
issn = {1080-6059},
mesh = {Cyclospora/*classification/*genetics ; Cyclosporiasis/*parasitology/transmission ; *DNA, Mitochondrial ; Genetic Markers ; Genetic Variation ; Genotyping Techniques ; Humans ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during cyclosporiasis outbreak investigations.},
}

Cyclospora/*classification/*genetics
Cyclosporiasis/*parasitology/transmission
*DNA, Mitochondrial
Genetic Markers
Genetic Variation
Genotyping Techniques
Humans
Mitochondria/*genetics
Phylogeny

@article {pmid31856711,
year = {2019},
author = {Guerra, D and Lopes-Lima, M and Froufe, E and Gan, HM and Ondina, P and Amaro, R and Klunzinger, MW and Callil, C and Prié, V and Bogan, AE and Stewart, DT and Breton, S},
title = {Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida).},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {229},
doi = {10.1186/s12862-019-1554-5},
pmid = {31856711},
issn = {1471-2148},
support = {NORTE-01-0145-FEDER-030286//ConBiomics/ ; RGPIN/435656-2013//Natural Sciences and Engineering Research Council of Canada (CA), Discovery Grants/ ; RGPIN/217175-2013//Natural Sciences and Engineering Research Council of Canada (CA), Discovery Grants/ ; SFRH/BD/115728/2016//FCT/ ; 09NAT/ES/000514//Life+ Margal Ulla/ ; },
abstract = {BACKGROUND: Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products.

RESULTS: We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features.

CONCLUSIONS: The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.},
}

@article {pmid31436541,
year = {2019},
author = {Watson, E and Ahmad, K and Fraser, CL},
title = {The neuro-ophthalmology of inherited myopathies.},
journal = {Current opinion in ophthalmology},
volume = {30},
number = {6},
pages = {476-483},
doi = {10.1097/ICU.0000000000000610},
pmid = {31436541},
issn = {1531-7021},
mesh = {Eye Diseases, Hereditary/diagnosis/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria, Muscle/*pathology ; Mitochondrial Myopathies/diagnosis/*genetics ; Oculomotor Muscles/*pathology ; Ophthalmoplegia, Chronic Progressive External/diagnosis/*genetics ; },
abstract = {PURPOSE OF REVIEW: Inherited myopathies, and in particular mitochondrial myopathies, are heterogeneous disorders, and ocular manifestations may be the presenting feature or offer important diagnostic clues. The ophthalmologist may be key to diagnosis, facilitating recognition of associated potentially life-threatening organ manifestations and an integral part of multidisciplinary care. This review, focusing especially on mitochondrial myopathies, provides updates on clinical features, diagnosis and recent therapeutic developments.

RECENT FINDINGS: Ptosis and/or ophthalmoplegia is present in over half of patients with mitochondrial disease, and associated clinical features imply specific genetic associations. Advances in next-generation sequencing have led to rapid evolution in the field, improving diagnosis rates, facilitating identification of novel genes, mutations and phenotypes, and providing important insights into disease mechanisms and therapeutic possibilities. Improved understanding of molecular mechanisms in inherited myopathies is enabling the development of experimental molecular therapies with clinical potential.

SUMMARY: Genetic advances are driving progress in the field of inherited myopathies, influencing diagnosis, understanding of disease and development of therapies. Recognition of key features can impact diagnosis and management of these important conditions.},
}

Eye Diseases, Hereditary/diagnosis/*genetics
High-Throughput Nucleotide Sequencing
Humans
Mitochondria, Muscle/*pathology
Mitochondrial Myopathies/diagnosis/*genetics
Oculomotor Muscles/*pathology
Ophthalmoplegia, Chronic Progressive External/diagnosis/*genetics

@article {pmid31855060,
year = {2019},
author = {Sekar, D and Johnson, J and Biruntha, M and Lakhmanan, G and Gurunathan, D and Ross, K},
title = {Biological and Clinical Relevance of microRNAs in Mitochondrial Diseases/Dysfunctions.},
journal = {DNA and cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/dna.2019.5013},
pmid = {31855060},
issn = {1557-7430},
abstract = {Mitochondrial dysfunction arises from an inadequate number of mitochondria, an inability to provide necessary substrates to mitochondria, or a dysfunction in their electron transport and a denosine triphosphate synthesis machinery. Occurrences of mitochondrial dysfunction are due to genetic or environmental changes in the mitochondria or in the nuclear DNA that codes mitochondrial components. Currently, drug options are available, yet no treatment exists in sight of this disease and needs a new insight into molecular and signaling pathways for this disease. microRNAs (miRNAs) are small, endogenous, and noncoding RNAs function as a master regulator of gene expression. The evolution of miRNAs in the past two decades emerged as a key regulator of gene expression that controls physiological pathological cellular differentiation processes, and metabolic homeostasis such as development and cancer. It has been known that miRNAs are a potential biomarker in both communicable and noncommunicable diseases. But, in the case of mitochondrial dysfunction in miRNAs, the number of studies and investigations are comparatively less than those on other diseases and dysfunctions. In this review, we have elaborated the roles of miRNAs in the mitochondrial diseases and dysfunctions.},
}

@article {pmid30807715,
year = {2019},
author = {Matsche, MA and Adams, CR and Blazer, VS},
title = {Newly Described Coccidia Goussia bayae from White Perch Morone americana: Morphology and Phylogenetics Support Emerging Taxonomy of Goussia within Piscine Hosts.},
journal = {The Journal of parasitology},
volume = {105},
number = {1},
pages = {1-10},
pmid = {30807715},
issn = {1937-2345},
mesh = {Animals ; Bass/*parasitology ; Bays ; Bile Ducts, Intrahepatic/parasitology ; Coccidiosis/parasitology/*veterinary ; DNA, Ribosomal/chemistry ; Eimeriidae/*classification/genetics/ultrastructure ; Electron Transport Complex IV/genetics ; Female ; Fish Diseases/*parasitology ; Gallbladder/parasitology ; Male ; Maryland ; Mitochondria/genetics ; Oocysts/ultrastructure ; Phylogeny ; Rivers ; Virginia ; },
abstract = {In March and April 2016, 150 white perch (Morone americana) were collected from various localities in Chesapeake Bay and examined for coccidia. A previously undescribed species of coccidia was observed in the hepatic bile ducts and gallbladder of all white perch (100%) examined. We describe this species using morphological characteristics, histology, and gene sequences of the small-subunit ribosomal DNA (rDNA), large-subunit rDNA, and mitochondrial genes cytochrome oxidase 1 (COI), cytochrome oxidase b (Cytb), and cytochrome oxidase 3 (COIII). Oocysts of Goussia bayae n. sp. were subspherical with a single-layered smooth wall and measured (length [L] × width [W]) 26.2 × 21.8 μm, with a L/W ratio of 1.2. A micropyle was present but a micropyle cap, polar granules, and oocyst residuum were absent. Each oocyst contained 4 sporocysts that were ellipsoidal and measured (L × W) 12.6 × 7.8 μm, with a L/W ratio of 1.6. A pair of sporozoites was present, but sporocysts lacked a Stieda body and residuua. Meronts and gamonts were epicellular in biliary epithelial cells and oocysts were coelozoic in hepatic and common bile ducts and gallbladder. This is the first report of Goussia spp. from white perch and the first mitochondrial DNA sequence reported from a Goussia species. Phylogenetic analysis indicates basal placement of G. bayae to Eimeriidae, Choleoeimeria, and Sarcocystidae.},
}

Animals
Bass/*parasitology
Bays
Bile Ducts, Intrahepatic/parasitology
Coccidiosis/parasitology/*veterinary
DNA, Ribosomal/chemistry
Eimeriidae/*classification/genetics/ultrastructure
Electron Transport Complex IV/genetics
Female
Fish Diseases/*parasitology
Gallbladder/parasitology
Male
Maryland
Mitochondria/genetics
Oocysts/ultrastructure
Phylogeny
Rivers
Virginia

@article {pmid30807709,
year = {2019},
author = {Léveillé, AN and Bland, SK and Carlton, K and Larouche, CB and Kenney, DG and Brouwer, ER and Lillie, BN and Barta, JR},
title = {Klossiella equi Infecting Kidneys of Ontario Horses: Life Cycle Features and Multilocus Sequence-Based Genotyping Confirm the Genus Klossiella Belongs In the Adeleorina (Apicomplexa: Coccidia).},
journal = {The Journal of parasitology},
volume = {105},
number = {1},
pages = {29-40},
pmid = {30807709},
issn = {1937-2345},
mesh = {Animals ; Coccidiosis/epidemiology/parasitology/*veterinary ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Eucoccidiida/*classification/genetics/growth & development ; Female ; Genotyping Techniques/veterinary ; Horse Diseases/epidemiology/*parasitology ; Horses ; Kidney/parasitology ; Kidney Diseases/epidemiology/parasitology/*veterinary ; Life Cycle Stages ; Male ; Mitochondria/genetics ; Multilocus Sequence Typing/veterinary ; Ontario/epidemiology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Species in the genus Klossiella Smith and Johnson, 1902 are unique among the suborder Adeleorina because they are monoxenous in mammals exclusively, whereas all other reported members of the Adeleorina use invertebrates as definitive hosts. Unlike other coccidia, all members of the Adeleorina undergo syzygy, the association of microgamonts and macrogamonts before maturation to gametes and syngamy. After fertilization, many members of the Adeleorina produce thin-walled polysporocystic oocysts. Despite being biologically similar to other members of the Adeleorina, the phylogenetic placement of the genus Klossiella has been questioned based on its unique host affinity. In the present study, 2 cases of Klossiella equi were reported from the kidneys of horses in Ontario. Details of the life cycle as well as mitochondrial and nuclear 18S ribosomal DNA (18S rDNA) sequences were analyzed to provide both morphological and molecular evidence for the phylogenetic placement of K. equi. Initially, various stages of the life cycle were identified in histological slides prepared from the kidney tissue, and DNA was isolated from the infected tissue. Polymerase chain reaction and Sanger sequencing were used to generate a complete mitochondrial genome sequence (6,569 bp) and a partial 18S rDNA sequence (1,443 bp). The K. equi 18S rDNA sequence was aligned with various publicly available apicomplexan 18S rDNA sequences. This alignment was used to generate a phylogenetic tree based on Bayesian inference. Multiple K. equi stages were identified including meronts, microgamonts, and macrogamonts associating in syzygy as well as thin-walled oocysts in various stages of sporogonic development. The 18S rDNA sequence of K. equi positioned within the monophyletic Adeleorina clade. The mitochondrial genome of K. equi contained 3 coding sequences for cytochrome c oxidase I, cytochrome c oxidase III, and cytochrome b as well as various fragmented ribosomal sequences. These components were arranged in a unique order that has not been observed in other apicomplexan mitochondrial genomes sequenced to date. Overall, it was concluded that there were sufficient morphological and molecular data to confirm the placement of K. equi and the genus Klossiella among the Adeleorina. The biological and molecular data obtained from these cases may assist with future studies evaluating the prevalence and life history of this seemingly underreported parasite and better define the impact of K. equi on the health of domestic and wild equids.},
}

Animals
Coccidiosis/epidemiology/parasitology/*veterinary
DNA, Ribosomal/chemistry
Electron Transport Complex IV/genetics
Eucoccidiida/*classification/genetics/growth & development
Female
Genotyping Techniques/veterinary
Horse Diseases/epidemiology/*parasitology
Horses
Kidney/parasitology
Kidney Diseases/epidemiology/parasitology/*veterinary
Life Cycle Stages
Male
Mitochondria/genetics
Multilocus Sequence Typing/veterinary
Ontario/epidemiology
Phylogeny
RNA, Ribosomal, 18S/genetics

@article {pmid31850200,
year = {2019},
author = {Tomasetti, M and Gaetani, S and Monaco, F and Neuzil, J and Santarelli, L},
title = {Epigenetic Regulation of miRNA Expression in Malignant Mesothelioma: miRNAs as Biomarkers of Early Diagnosis and Therapy.},
journal = {Frontiers in oncology},
volume = {9},
number = {},
pages = {1293},
doi = {10.3389/fonc.2019.01293},
pmid = {31850200},
issn = {2234-943X},
abstract = {Asbestos exposure leads to epigenetic and epigenomic modifications that, in association with ROS-induced DNA damage, contribute to cancer onset. Few miRNAs epigenetically regulated in MM have been described in literature; miR-126, however, is one of them, and its expression is regulated by epigenetic mechanisms. Asbestos exposure induces early changes in the miRNAs, which are reversibly expressed as protective species, and their inability to reverse reflects the inability of the cells to restore the physiological miRNA levels despite the cessation of carcinogen exposure. Changes in miRNA expression, which results from genetic/epigenetic changes during tumor formation and evolution, can be detected in fluids and used as cancer biomarkers. This article has reviewed the epigenetic mechanisms involved in miRNA expression in MM, focusing on their role as biomarkers of early diagnosis and therapeutic effects.},
}

@article {pmid31842897,
year = {2019},
author = {Souza, F and Rodrigues, R and Reis, E and Lima, M and La Scola, B and Abrahão, J},
title = {In-depth analysis of the replication cycle of Orpheovirus.},
journal = {Virology journal},
volume = {16},
number = {1},
pages = {158},
doi = {10.1186/s12985-019-1268-8},
pmid = {31842897},
issn = {1743-422X},
support = {01//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {BACKGROUND: After the isolation of Acanthamoeba polyphaga mimivirus (APMV), the study and search for new giant viruses has been intensified. Most giant viruses are associated with free-living amoebae of the genus Acanthamoeba; however other giant viruses have been isolated in Vermamoeba vermiformis, such as Faustovirus, Kaumoebavirus and Orpheovirus. These studies have considerably expanded our knowledge about the diversity, structure, genomics, and evolution of giant viruses. Until now, there has been only one Orpheovirus isolate, and many aspects of its life cycle remain to be elucidated.

METHODS: In this study, we performed an in-depth characterization of the replication cycle and particles of Orpheovirus by transmission and scanning electron microscopy, optical microscopy and IF assays.

RESULTS: We observed, through optical and IF microscopy, morphological changes in V. vermiformis cells during Orpheovirus infection, as well as increased motility at 12 h post infection (h.p.i.). The viral factory formation and viral particle morphogenesis were analysed by transmission electron microscopy, revealing mitochondria and membrane recruitment into and around the electron-lucent viral factories. Membrane traffic inhibitor (Brefeldin A) negatively impacted particle morphogenesis. The first structure observed during particle morphogenesis was crescent-shaped bodies, which extend and are filled by the internal content until the formation of multi-layered mature particles. We also observed the formation of defective particles with different shapes and sizes. Virological assays revealed that viruses are released from the host by exocytosis at 12 h.p.i., which is associated with an increase of particle counts in the supernatant.

CONCLUSIONS: The results presented here contribute to a better understanding of the biology, structures and important steps in the replication cycle of Orpheovirus.},
}

@article {pmid31519208,
year = {2019},
author = {Wang, T and Zhang, S and Pei, T and Yu, Z and Liu, J},
title = {Tick mitochondrial genomes: structural characteristics and phylogenetic implications.},
journal = {Parasites & vectors},
volume = {12},
number = {1},
pages = {451},
doi = {10.1186/s13071-019-3705-3},
pmid = {31519208},
issn = {1756-3305},
support = {31672365//The National Natural Science Foundation of China/ ; BJ2016032//The Natural Science Research Programs of the Educational Department of Hebei Province/ ; L2018J04//The Science Foundation of Hebei Normal University/ ; C2019205064//the Natural Science Foundation of Hebei Province/ ; },
mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Ticks/*genetics ; },
abstract = {Ticks are obligate blood-sucking arachnid ectoparasites from the order Acarina, and many are notorious as vectors of a wide variety of zoonotic pathogens. However, the systematics of ticks in several genera is still controversial. The mitochondrial genome (mt-genome) has been widely used in arthropod phylogeny, molecular evolution and population genetics. With the development of sequencing technologies, an increasing number of tick mt-genomes have been sequenced and annotated. To date, 63 complete tick mt-genomes are available in the NCBI database, and these genomes have become an increasingly important genetic resource and source of molecular markers in phylogenetic studies of ticks in recent years. The present review summarizes all available complete mt-genomes of ticks in the NCBI database and analyses their characteristics, including structure, base composition and gene arrangement. Furthermore, a phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes from ticks. The results will provide important clues for deciphering new tick mt-genomes and establish a foundation for subsequent taxonomic research.},
}

Animals
Base Composition
Gene Order
*Genome, Mitochondrial
Mitochondria/*genetics
Phylogeny
Ticks/*genetics

@article {pmid31371715,
year = {2019},
author = {Mackintosh, A and Laetsch, DR and Hayward, A and Charlesworth, B and Waterfall, M and Vila, R and Lohse, K},
title = {The determinants of genetic diversity in butterflies.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3466},
doi = {10.1038/s41467-019-11308-4},
pmid = {31371715},
issn = {2041-1723},
mesh = {Animals ; Biodiversity ; Body Size ; Butterflies/*classification/*genetics ; Chromosomes ; Evolution, Molecular ; Genetic Drift ; Genetic Variation/*genetics ; Genome ; Genome Size ; Karyotype ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Density ; Recombination, Genetic ; *Selection, Genetic ; },
abstract = {Under the neutral theory, genetic diversity is expected to increase with population size. While comparative analyses have consistently failed to find strong relationships between census population size and genetic diversity, a recent study across animals identified a strong correlation between propagule size and genetic diversity, suggesting that r-strategists that produce many small offspring, have greater long-term population sizes. Here we compare genome-wide genetic diversity across 38 species of European butterflies (Papilionoidea), a group that shows little variation in reproductive strategy. We show that genetic diversity across butterflies varies over an order of magnitude and that this variation cannot be explained by differences in current abundance, propagule size, host or geographic range. Instead, neutral genetic diversity is negatively correlated with body size and positively with the length of the genetic map. This suggests that genetic diversity is determined both by differences in long-term population size and the effect of selection on linked sites.},
}

Animals
Biodiversity
Body Size
Butterflies/*classification/*genetics
Chromosomes
Evolution, Molecular
Genetic Drift
Genetic Variation/*genetics
Genome
Genome Size
Karyotype
Mitochondria/genetics
Phylogeny
Phylogeography
Population Density
Recombination, Genetic
*Selection, Genetic

@article {pmid31204704,
year = {2019},
author = {Mothay, D and Ramesh, KV},
title = {Evolutionary history and genetic diversity study of heat-shock protein 60 of Rhizophagus irregularis.},
journal = {Journal of genetics},
volume = {98},
number = {2},
pages = {},
pmid = {31204704},
issn = {0973-7731},
mesh = {Chaperonin 60/*genetics/metabolism ; Codon ; Databases, Genetic ; Dyslexia/genetics ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; Glomeromycota/classification/*genetics/metabolism ; Humans ; Meta-Analysis as Topic ; Mitochondria/genetics/metabolism ; Odds Ratio ; Phylogeny ; Polymorphism, Genetic ; Synteny ; },
abstract = {Despite the ubiquitous occurrence of heat-shock protein 60 (Hsp60) and their role in maintenance of cell activity and integrity, this protein remains poorly characterized in many of the symbiotic soil mycorrhizal fungi such as Rhizophagus irregularis. Thus, in the current study, an attempt has been made to elucidate the evolutionary history, time of divergence followed by estimation of population genetic parameters of hsp60 using R. irregularis as a model organism. Sequence alignment reported here identified several close homologues for hsp60 (gene) and Hsp60 (protein) from diverse taxa, while the output from protein-based phylogenetic tree indicates that mitochondrial Hsp60 of R. irregularis shares close evolutionary relationship with classical α-proteobacteria. This is perhaps the first line of evidence elucidating the likelihood of hsp60 from fungal taxa sharing a close evolutionary relationship with classical α-proteobacteria as a common ancestor. Comprehensive analysis of mitochondrial hsp60 from selected fungal taxa from the evolutionary point of view explains the possibility of gene duplication and or horizontal gene transfer of this gene across various fungal species. Synteny relationships and population genetics credibly explain high genetic variability associated with fungal hsp60 presumably brought by random genetic recombination events. The results presented here also confirm a high level of genetic differentiation of hsp60 among all the three fungal populations analysed. In this context, the outcome of the current study, basedon computational approach, stands as a testimony for explaining the possibility of increased genetic differentiation experienced by hsp60 of R. irregularis.},
}

Chaperonin 60/*genetics/metabolism
Codon
Databases, Genetic
Dyslexia/genetics
*Evolution, Molecular
*Genetic Variation
Genetics, Population
Glomeromycota/classification/*genetics/metabolism
Humans
Meta-Analysis as Topic
Mitochondria/genetics/metabolism
Odds Ratio
Phylogeny
Polymorphism, Genetic
Synteny

@article {pmid30981810,
year = {2019},
author = {Pazmiño, DA and van Herderden, L and Simpfendorfer, CA and Junge, C and Donnellan, SC and Hoyos-Padilla, EM and Duffy, CAJ and Huveneers, C and Gillanders, BM and Butcher, PA and Maes, GE},
title = {Introgressive hybridisation between two widespread sharks in the east Pacific region.},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {119-127},
doi = {10.1016/j.ympev.2019.04.013},
pmid = {30981810},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; California ; Computer Simulation ; DNA, Mitochondrial/genetics ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sample Size ; Sharks/*genetics ; },
abstract = {With just a handful of documented cases of hybridisation in cartilaginous fishes, shark hybridisation remains poorly investigated. Small amounts of admixture have been detected between Galapagos (Carcharhinus galapagensis) and dusky (Carcharhinus obscurus) sharks previously, generating a hypothesis of ongoing hybridisation. We sampled a large number of individuals from areas where the species co-occur (contact zones) across the Pacific Ocean and used both mitochondrial and nuclear-encoded SNPs to examine genetic admixture and introgression between the two species. Using empirical analytical approaches and simulations, we first developed a set of 1873 highly informative SNPs for these two species to evaluate the degree of admixture between them. Overall, results indicate a high discriminatory power of nuclear SNPs (FST = 0.47, p < 0.05) between the two species, unlike mitochondrial DNA (ΦST = 0.00 p > 0.05), which failed to differentiate these species. We identified four hybrid individuals (∼1%) and detected bi-directional introgression between C. galapagensis and C. obscurus in the Gulf of California along the east Pacific coast of the Americas. We emphasize the importance of including a combination of mtDNA and diagnostic nuclear markers to properly assess species identification, detect patterns of hybridisation, and better inform management and conservation of these sharks, especially given the morphological similarities within the genus Carcharhinus.},
}

Animals
Bayes Theorem
California
Computer Simulation
DNA, Mitochondrial/genetics
Geography
*Hybridization, Genetic
Mitochondria/genetics
Pacific Ocean
Phylogeny
Polymorphism, Single Nucleotide/genetics
Sample Size
Sharks/*genetics

@article {pmid30897177,
year = {2019},
author = {Liao, L and Dong, T and Liu, X and Dong, Z and Qiu, X and Rong, Y and Sun, G and Wang, Z},
title = {Effect of nitrogen supply on nitrogen metabolism in the citrus cultivar 'Huangguogan'.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213874},
doi = {10.1371/journal.pone.0213874},
pmid = {30897177},
issn = {1932-6203},
mesh = {Citrus/growth & development/*metabolism ; Cytoplasm/metabolism ; Fruit/metabolism ; Gene Expression Regulation, Plant ; Glutamate Dehydrogenase/classification/genetics/metabolism ; Glutamate-Ammonia Ligase/classification/genetics/metabolism ; Nitrate Reductase/classification/genetics/metabolism ; Nitrogen/*metabolism ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/classification/genetics/*metabolism ; Plant Roots/metabolism ; Seedlings/growth & development/metabolism ; },
abstract = {Nitrogen metabolism in citrus has received increased attention due to its effects on plant growth and productivity. However, little is known about the effects of nitrogen fertilization on nitrogen metabolism in young trees of citrus cultivar 'Huangguogan' (Citrus reticulata × Citrus sinensis). Here, genes encoding nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate dehydrogenase (GDH), and asparagine synthetase (AS), represented as HgNR, HgNiR, HgGS, HgGDH, and HgAS, respectively, were cloned from Huangguogan. Deduced protein sequences were analyzed and proteins were confirmed to be localized in their respective cellular organelles. Moreover, pot-cultured 'Huangguogan' seedlings were fertilized with 0 (N1), 1.36 (N2), 1.81 (N3), 2.26 (N4), or 2.72 (N5) kg N/year, for 12 months. Enzyme activity and enzyme-gene expression were studied in roots, leaves, and fruits at different stages. Finally, the effects of N application rate on root activity, leaf N, soluble protein, yield, and fruit quality at the ripening stage were measured. The results showed that: 1) HgNR, HgNiR, HgGDH, and HgAS gene products were found mainly in the cytoplasm and plasma membrane, while HgGS gene product was found mainly in cytoplasm and mitochondria. 2) Gene expression and enzyme activity differed among plant organs. As the root is in permanent direct contact with the soil we suggest that root gene expression and enzyme activity can be used as reference to determine N application rate. 3) Yield, fruit quality, enzyme activity, and enzyme-related gene expression were considerably lower at low than at high-N supply. However, they were all inhibited by excess nitrogen (i.e., 2.72 kg/year). Therefore, we recommend 1.81 kg N/year as the optimal N application rate for young 'Huangguogan' trees.},
}

Citrus/growth & development/*metabolism
Cytoplasm/metabolism
Fruit/metabolism
Gene Expression Regulation, Plant
Glutamate Dehydrogenase/classification/genetics/metabolism
Glutamate-Ammonia Ligase/classification/genetics/metabolism
Nitrate Reductase/classification/genetics/metabolism
Nitrogen/*metabolism
Phylogeny
Plant Leaves/metabolism
Plant Proteins/classification/genetics/*metabolism
Plant Roots/metabolism
Seedlings/growth & development/metabolism

@article {pmid30893849,
year = {2019},
author = {Ding, F and Cheng, J and Fu, Y and Chen, T and Li, B and Jiang, D and Xie, J},
title = {Early Transcriptional Response to DNA Virus Infection in Sclerotinia sclerotiorum.},
journal = {Viruses},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/v11030278},
pmid = {30893849},
issn = {1999-4915},
mesh = {Ascomycota/*genetics/pathogenicity/*virology ; DNA Viruses/*genetics ; *Gene Expression Profiling ; Hyphae/genetics/virology ; Phylogeny ; Sequence Analysis, DNA ; Virion/genetics ; Virulence ; },
abstract = {We previously determined that virions of Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 (SsHADV-1) could directly infect hyphae of Sclerotinia sclerotiorum, resulting in hypovirulence of the fungal host. However, the molecular mechanisms of SsHADV-1 virions disruption of the fungal cell wall barrier and entrance into the host cell are still unclear. To investigate the early response of S. sclerotiorum to SsHADV-1 infection, S. sclerotiorum hyphae were inoculated with purified SsHADV-1 virions. The pre- and post-infection hyphae were collected at one⁻three hours post-inoculation for transcriptome analysis. Further, bioinformatic analysis showed that differentially expressed genes (DEGs) regulated by SsHADV-1 infection were identified in S. sclerotiorum. In total, 187 genes were differentially expressed, consisting of more up-regulated (114) than down-regulated (73) genes. The identified DEGs were involved in several important pathways. Metabolic processes, biosynthesis of antibiotics, and secondary metabolites were the most affected categories in S. sclerotiorum upon SsHADV-1 infection. Cell structure analysis suggested that 26% of the total DEGs were related to membrane tissues. Furthermore, 10 and 27 DEGs were predicted to be located in the cell membrane and mitochondria, respectively. Gene ontology enrichment analyses of the DEGs were performed, followed by functional annotation of the genes. Interestingly, one third of the annotated functional DEGs could be involved in the Ras-small G protein signal transduction pathway. These results revealed that SsHADV-1 virions may be able to bind host membrane proteins and influence signal transduction through Ras-small G protein-coupled receptors during early infection, providing new insight towards the molecular mechanisms of virions infection in S. sclerotiorum.},
}

Ascomycota/*genetics/pathogenicity/*virology
DNA Viruses/*genetics
*Gene Expression Profiling
Hyphae/genetics/virology
Phylogeny
Sequence Analysis, DNA
Virion/genetics
Virulence

@article {pmid30466901,
year = {2019},
author = {Hampl, V and Čepička, I and Eliáš, M},
title = {Was the Mitochondrion Necessary to Start Eukaryogenesis?.},
journal = {Trends in microbiology},
volume = {27},
number = {2},
pages = {96-104},
doi = {10.1016/j.tim.2018.10.005},
pmid = {30466901},
issn = {1878-4380},
mesh = {Adenosine Triphosphate ; Archaea/physiology ; *Biological Evolution ; Eukaryota/genetics/*physiology ; Eukaryotic Cells/*physiology ; Genome ; Mitochondria/genetics/*physiology ; Phagocytosis ; Prokaryotic Cells/physiology ; Symbiosis ; },
abstract = {Arguments based on cell energetics favour the view that a mitochondrion capable of oxidative phosphorylation was a prerequisite for the evolution of other features of the eukaryotic cell, including increased volume, genome size and, eventually, phagotrophy. Contrary to this we argue that: (i) extant amitochondriate eukaryotes possess voluminous phagotrophic cells with large genomes; (ii) picoeukaryotes demonstrate that phagotrophy is feasible at prokaryotic cell sizes; and (iii) the assumption that evolution of complex features requires extra ATP, often mentioned in this context, is unfounded and should not be used in such considerations. We claim that the diversity of cell organisations and functions observed today in eukaryotes gives no reason to postulate that a mitochondrion must have preceded phagocytosis in eukaryogenesis.},
}

Adenosine Triphosphate
Archaea/physiology
*Biological Evolution
Eukaryota/genetics/*physiology
Eukaryotic Cells/*physiology
Genome
Mitochondria/genetics/*physiology
Phagocytosis
Prokaryotic Cells/physiology
Symbiosis

@article {pmid30403999,
year = {2018},
author = {Wettmarshausen, J and Goh, V and Huang, KT and Arduino, DM and Tripathi, U and Leimpek, A and Cheng, Y and Pittis, AA and Gabaldón, T and Mokranjac, D and Hajnóczky, G and Perocchi, F},
title = {MICU1 Confers Protection from MCU-Dependent Manganese Toxicity.},
journal = {Cell reports},
volume = {25},
number = {6},
pages = {1425-1435.e7},
doi = {10.1016/j.celrep.2018.10.037},
pmid = {30403999},
issn = {2211-1247},
mesh = {Apoptosis/drug effects ; Calcium Channels/*metabolism ; Calcium-Binding Proteins/*metabolism ; Cation Transport Proteins/*metabolism ; *Cytoprotection/drug effects ; Eukaryota ; Evolution, Molecular ; HEK293 Cells ; HeLa Cells ; Humans ; Iron/toxicity ; Manganese/*toxicity ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Phylogeny ; Saccharomyces cerevisiae/metabolism ; Stress, Physiological/drug effects ; },
abstract = {The mitochondrial calcium uniporter is a highly selective ion channel composed of species- and tissue-specific subunits. However, the functional role of each component still remains unclear. Here, we establish a synthetic biology approach to dissect the interdependence between the pore-forming subunit MCU and the calcium-sensing regulator MICU1. Correlated evolutionary patterns across 247 eukaryotes indicate that their co-occurrence may have conferred a positive fitness advantage. We find that, while the heterologous reconstitution of MCU and EMRE in vivo in yeast enhances manganese stress, this is prevented by co-expression of MICU1. Accordingly, MICU1 deletion sensitizes human cells to manganese-dependent cell death by disinhibiting MCU-mediated manganese uptake. As a result, manganese overload increases oxidative stress, which can be effectively prevented by NAC treatment. Our study identifies a critical contribution of MICU1 to the uniporter selectivity, with important implications for patients with MICU1 deficiency, as well as neurological disorders arising upon chronic manganese exposure.},
}

Apoptosis/drug effects
Calcium Channels/*metabolism
Calcium-Binding Proteins/*metabolism
Cation Transport Proteins/*metabolism
*Cytoprotection/drug effects
Eukaryota
Evolution, Molecular
HEK293 Cells
HeLa Cells
Humans
Iron/toxicity
Manganese/*toxicity
Mitochondria/metabolism
Mitochondrial Membrane Transport Proteins/*metabolism
Phylogeny
Saccharomyces cerevisiae/metabolism
Stress, Physiological/drug effects

@article {pmid30279542,
year = {2018},
author = {Severgnini, M and Lazzari, B and Capra, E and Chessa, S and Luini, M and Bordoni, R and Castiglioni, B and Ricchi, M and Cremonesi, P},
title = {Genome sequencing of Prototheca zopfii genotypes 1 and 2 provides evidence of a severe reduction in organellar genomes.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14637},
pmid = {30279542},
issn = {2045-2322},
mesh = {Chromosome Mapping ; DNA-Directed RNA Polymerases/genetics ; Genome, Mitochondrial ; Genome, Plant ; Genome, Plastid ; Host-Pathogen Interactions/genetics ; Mitochondria/*genetics ; Photosynthesis/*genetics ; Plastids/*genetics ; Prototheca/*classification/*genetics ; },
abstract = {Prototheca zopfii (P. zopfii, class Trebouxiophyceae, order Chlorellales, family Chlorellaceae), a non-photosynthetic predominantly free-living unicellular alga, is one of the few pathogens belonging to the plant kingdom. This alga can affect many vertebrate hosts, sustaining systemic infections and diseases such as mastitis in cows. The aim of our work was to sequence and assemble the P. zopfii genotype 1 and genotype 2 mitochondrial and plastid genomes. Remarkably, the P. zopfii mitochondrial (38 Kb) and plastid (28 Kb) genomes are models of compaction and the smallest known in the Trebouxiophyceae. As expected, the P. zopfii genotype 1 and 2 plastid genomes lack all the genes involved in photosynthesis, but, surprisingly, they also lack those coding for RNA polymerases. Our results showed that plastid genes are actively transcribed in P. zopfii, which suggests that the missing RNA polymerases are substituted by nuclear-encoded paralogs. The simplified architecture and highly-reduced gene complement of the P. zopfii mitochondrial and plastid genomes are closer to those of P. stagnora and the achlorophyllous obligate parasite Helicosporidium than to those of P. wickerhamii or P. cutis. This similarity is also supported by maximum likelihood phylogenetic analyses inferences. Overall, the P. zopfii sequences reported here, which include nuclear genome drafts for both genotypes, will help provide both a deeper understanding of the evolution of Prototheca spp. and insights into the corresponding host/pathogen interactions.},
}

Chromosome Mapping
DNA-Directed RNA Polymerases/genetics
Genome, Mitochondrial
Genome, Plant
Genome, Plastid
Host-Pathogen Interactions/genetics
Mitochondria/*genetics
Photosynthesis/*genetics
Plastids/*genetics
Prototheca/*classification/*genetics

@article {pmid31667843,
year = {2019},
author = {Gerke, P and Szövényi, P and Neubauer, A and Lenz, H and Gutmann, B and McDowell, R and Small, I and Schallenberg-Rüdinger, M and Knoop, V},
title = {Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.16297},
pmid = {31667843},
issn = {1469-8137},
support = {SCHA1952/2-1//German Research Foundation/ ; 160004/SNSF_/Swiss National Science Foundation/Switzerland ; 131726/SNSF_/Swiss National Science Foundation/Switzerland ; //Georges and Antoine Claraz Foundation (Switzerland)/ ; //US National Science Foundation/ ; //Forschungskredit/ ; //University Research Priority Program 'Evolution in Action' of the University of Zurich/ ; },
abstract = {Hornworts are crucial to understand the phylogeny of early land plants. The emergence of 'reverse' U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort-tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the 'classic' DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.},
}

@article {pmid31815198,
year = {2019},
author = {Bargelloni, L and Babbucci, M and Ferraresso, S and Papetti, C and Vitulo, N and Carraro, R and Pauletto, M and Santovito, G and Lucassen, M and Mark, FC and Zane, L and Patarnello, T},
title = {Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {443},
doi = {10.1038/s42003-019-0685-y},
pmid = {31815198},
issn = {2399-3642},
abstract = {Antarctic fish belonging to Notothenioidei represent an extraordinary example of radiation in the cold. In addition to the absence of hemoglobin, icefish show a number of other striking peculiarities including large-diameter blood vessels, high vascular densities, mitochondria-rich muscle cells, and unusual mitochondrial architecture. In order to investigate the bases of icefish adaptation to the extreme Southern Ocean conditions we sequenced the complete genome of the icefish Chionodraco myersi. Comparative analyses of the icefish genome with those of other teleost species, including two additional white-blooded and five red-blooded notothenioids, provided a new perspective on the evolutionary loss of globin genes. Muscle transcriptome comparative analyses against red-blooded notothenioids as well as temperate fish revealed the peculiar regulation of genes involved in mitochondrial function in icefish. Gene duplication and promoter sequence divergence were identified as genome-wide patterns that likely contributed to the broad transcriptional program underlying the unique features of icefish mitochondria.},
}

@article {pmid31806760,
year = {2019},
author = {Rosenberg, A and Luth, MR and Winzeler, EA and Behnke, M and Sibley, LD},
title = {Evolution of resistance in vitro reveals mechanisms of artemisinin activity in Toxoplasma gondii.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1914732116},
pmid = {31806760},
issn = {1091-6490},
abstract = {Artemisinins are effective against a variety of parasites and provide the first line of treatment for malaria. Laboratory studies have identified several mechanisms for artemisinin resistance in Plasmodium falciparum, including mutations in Kelch13 that are associated with delayed clearance in some clinical isolates, although other mechanisms are likely involved. To explore other potential mechanisms of resistance in parasites, we took advantage of the genetic tractability of Toxoplasma gondii, a related parasite that shows moderate sensitivity to artemisinin. Resistant populations of T. gondii were selected by culture in increasing concentrations and whole-genome sequencing identified several nonconservative point mutations that emerged in the population and were fixed over time. Genome editing using CRISPR/Cas9 was used to introduce point mutations conferring amino acid changes in a serine protease homologous to DegP and a serine/threonine protein kinase of unknown function. Single and double mutations conferred a competitive advantage over wild-type parasites in the presence of drug, despite not changing EC50 values. Additionally, the evolved resistant lines showed dramatic amplification of the mitochondria genome, including genes encoding cytochrome b and cytochrome c oxidase I. Prior studies in yeast and mammalian tumor cells implicate the mitochondrion as a target of artemisinins, and treatment of wild-type parasites with high concentrations of drug decreased mitochondrial membrane potential, a phenotype that was stably altered in the resistant parasites. These findings extend the repertoire of mutations associated with artemisinin resistance and suggest that the mitochondrion may be an important target of inhibition of resistance in T. gondii.},
}

@article {pmid31797248,
year = {2019},
author = {Hein, A and Brenner, S and Polsakiewicz, M and Knoop, V},
title = {The dual-targeted RNA editing factor AEF1 is universally conserved among angiosperms and reveals only minor adaptations upon loss of its chloroplast or its mitochondrial target.},
journal = {Plant molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11103-019-00940-9},
pmid = {31797248},
issn = {1573-5028},
abstract = {KEY MESSAGE: Upon loss of either its chloroplast or mitochondrial target, a uniquely dual-targeted factor for C-to-U RNA editing in angiosperms reveals low evidence for improved molecular adaptation to its remaining target. RNA-binding pentatricopeptide repeat (PPR) proteins specifically recognize target sites for C-to-U RNA editing in the transcriptomes of plant chloroplasts and mitochondria. Among more than 80 PPR-type editing factors that have meantime been characterized, AEF1 (or MPR25) is a special case given its dual targeting to both organelles and addressing an essential mitochondrial (nad5eU1580SL) and an essential chloroplast (atpFeU92SL) RNA editing site in parallel in Arabidopsis. Here, we explored the angiosperm-wide conservation of AEF1 and its two organelle targets. Despite numerous independent losses of the chloroplast editing site by C-to-T conversion and at least four such conversions at the mitochondrial target site in other taxa, AEF1 remains consistently conserved in more than 120 sampled angiosperm genomes. Not a single case of simultaneous loss of the chloroplast and mitochondrial editing target or of AEF1 disintegration or loss could be identified, contrasting previous findings for editing factors targeted to only one organelle. Like in most RNA editing factors, the PPR array of AEF1 reveals potential for conceptually "improved fits" to its targets according to the current PPR-RNA binding code. Surprisingly, we observe only minor evidence for adaptation to the mitochondrial target also after deep losses of the chloroplast target among Asterales, Caryophyllales and Poales or, vice versa, for the remaining chloroplast target after a deep loss of the mitochondrial target among Malvales. The evolutionary observations support the notion that PPR-RNA mismatches may be essential for proper function of editing factors.},
}

@article {pmid31794060,
year = {2019},
author = {Kumar, S and Nandi, A and Mahesh, A and Sinha, S and Flores, E and Chakrabarti, R},
title = {Novel function of ∆Np63 in cell polarity and metabolism in pubertal mammary gland development.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.13703},
pmid = {31794060},
issn = {1873-3468},
abstract = {The ∆Np63 isoform of the p53-family transcription factor Trp63 is a key regulator of mammary epithelial stem cells that is involved in breast cancer development. To investigate the role of ∆Np63 at different stages of normal mammary gland development, we generated a ∆Np63 inducible conditional knockout (cKO) mouse model. We demonstrate that deletion of ∆Np63 at puberty results in depletion of mammary stem cell-enriched basal cells, reduces expression of E-cadherin and β-catenin, and leads to a closed ductal lumen. RNA-sequencing analysis reveals reduced expression of oxidative phosphorylation (OXPHOS)-associated proteins and desmosomal polarity proteins. Functional assays show reduced numbers of mitochondria in the mammary epithelial cells of ΔNp63 cKO compared to wildtype, supporting the reduced OXPHOS phenotype. These findings identify a novel role for ∆Np63 in cellular metabolism and mammary epithelial cell polarity.},
}

@article {pmid31787040,
year = {2020},
author = {Bettinazzi, S and Nadarajah, S and Dalpé, A and Milani, L and Blier, PU and Breton, S},
title = {Linking paternally inherited mtDNA variants and sperm performance.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1790},
pages = {20190177},
doi = {10.1098/rstb.2019.0177},
pmid = {31787040},
issn = {1471-2970},
abstract = {Providing robust links between mitochondrial genotype and phenotype is of major importance given that mitochondrial DNA (mtDNA) variants can affect reproductive success. Because of the strict maternal inheritance (SMI) of mitochondria in animals, haplotypes that negatively affect male fertility can become fixed in populations. This phenomenon is known as 'mother's curse'. Doubly uniparental inheritance (DUI) of mitochondria is a stable exception in bivalves, which entails two mtDNA lineages that evolve independently and are transmitted separately through oocytes and sperm. This makes the DUI mitochondrial lineages subject to different sex-specific selective sieves during mtDNA evolution, thus DUI is a unique model to evaluate how direct selection on sperm mitochondria could contribute to male reproductive fitness. In this study, we tested the impact of mtDNA variants on sperm performance and bioenergetics in DUI and SMI species. Analyses also involved measures of sperm performance following inhibition of main energy pathways and sperm response to oocyte presence. Compared to SMI, DUI sperm exhibited (i) low speed and linearity, (ii) a strict OXPHOS-dependent strategy of energy production, and (iii) a partial metabolic shift towards fermentation following egg detection. Discussion embraces the adaptive value of mtDNA variation and suggests a link between male-energetic adaptation, fertilization success and paternal mitochondria preservation. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.},
}

@article {pmid31787038,
year = {2020},
author = {Nagarajan-Radha, V and Aitkenhead, I and Clancy, DJ and Chown, SL and Dowling, DK},
title = {Sex-specific effects of mitochondrial haplotype on metabolic rate in Drosophila melanogaster support predictions of the Mother's Curse hypothesis.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1790},
pages = {20190178},
doi = {10.1098/rstb.2019.0178},
pmid = {31787038},
issn = {1471-2970},
abstract = {Evolutionary theory proposes that maternal inheritance of mitochondria will facilitate the accumulation of mitochondrial DNA (mtDNA) mutations that are harmful to males but benign or beneficial to females. Furthermore, mtDNA haplotypes sampled from across a given species distribution are expected to differ in the number and identity of these 'male-harming' mutations they accumulate. Consequently, it is predicted that the genetic variation which delineates distinct mtDNA haplotypes of a given species should confer larger phenotypic effects on males than females (reflecting mtDNA mutations that are male-harming, but female-benign), or sexually antagonistic effects (reflecting mutations that are male-harming, but female-benefitting). These predictions have received support from recent work examining mitochondrial haplotypic effects on adult life-history traits in Drosophila melanogaster. Here, we explore whether similar signatures of male-bias or sexual antagonism extend to a key physiological trait-metabolic rate. We measured the effects of mitochondrial haplotypes on the amount of carbon dioxide produced by individual flies, controlling for mass and activity, across 13 strains of D. melanogaster that differed only in their mtDNA haplotype. The effects of mtDNA haplotype on metabolic rate were larger in males than females. Furthermore, we observed a negative intersexual correlation across the haplotypes for metabolic rate. Finally, we uncovered a male-specific negative correlation, across haplotypes, between metabolic rate and longevity. These results are consistent with the hypothesis that maternal mitochondrial inheritance has led to the accumulation of a sex-specific genetic load within the mitochondrial genome, which affects metabolic rate and that may have consequences for the evolution of sex differences in life history. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.},
}

@article {pmid31787037,
year = {2020},
author = {Camus, MF and O'Leary, M and Reuter, M and Lane, N},
title = {Impact of mitonuclear interactions on life-history responses to diet.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1790},
pages = {20190416},
doi = {10.1098/rstb.2019.0416},
pmid = {31787037},
issn = {1471-2970},
abstract = {Mitochondria are central to both energy metabolism and biosynthesis. Mitochondrial function could therefore influence resource allocation. Critically, mitochondrial function depends on interactions between proteins encoded by the mitochondrial and nuclear genomes. Severe incompatibilities between these genomes can have pervasive effects on both fitness and longevity. How milder deficits in mitochondrial function affect life-history trade-offs is less well understood. Here, we analyse how mitonuclear interactions affect the trade-off between fecundity and longevity in Drosophila melanogaster. We consider a panel of 10 different mitochondrial DNA haplotypes against two contrasting nuclear backgrounds (w1118 (WE) and Zim53 (ZIM)) in response to high-protein versus standard diet. We report strikingly different responses between the two nuclear backgrounds. WE females have higher fecundity and decreased longevity on high protein. ZIM females have much greater fecundity and shorter lifespan than WE flies on standard diet. High protein doubled their fecundity with no effect on longevity. Mitochondrial haplotype reflected nuclear life-history trade-offs, with a negative correlation between longevity and fecundity in WE flies and no correlation in ZIM flies. Mitonuclear interactions had substantial effects but did not reflect genetic distance between mitochondrial haplotypes. We conclude that mitonuclear interactions can have significant impact on life-history trade-offs, but their effects are not predictable by relatedness. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.},
}

@article {pmid31553224,
year = {2019},
author = {Seligmann, H},
title = {Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry?.},
journal = {DNA and cell biology},
volume = {38},
number = {11},
pages = {1257-1268},
doi = {10.1089/dna.2019.4858},
pmid = {31553224},
issn = {1557-7430},
mesh = {Adaptive Immunity/genetics ; Chloroplasts/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions/genetics/immunology ; Immune Evasion/genetics ; Mitochondria/*genetics ; Molecular Mimicry/*physiology ; Organelles/genetics ; Phycodnaviridae/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Synteny/*genetics ; },
abstract = {Recent analyses suggest bacterial and/or mitochondrion-like ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond common ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.},
}

Adaptive Immunity/genetics
Chloroplasts/*genetics
*Evolution, Molecular
Genome, Mitochondrial/genetics
Genome, Viral/genetics
Host-Pathogen Interactions/genetics/immunology
Immune Evasion/genetics
Mitochondria/*genetics
Molecular Mimicry/*physiology
Organelles/genetics
Phycodnaviridae/*genetics
Phylogeny
Sequence Analysis, DNA
Synteny/*genetics

@article {pmid30639162,
year = {2019},
author = {López Rivero, AS and Rossi, MA and Ceccarelli, EA and Catalano-Dupuy, DL},
title = {A bacterial 2[4Fe4S] ferredoxin as redox partner of the plastidic-type ferredoxin-NADP+ reductase from Leptospira interrogans.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1863},
number = {4},
pages = {651-660},
doi = {10.1016/j.bbagen.2019.01.004},
pmid = {30639162},
issn = {1872-8006},
mesh = {Amino Acid Sequence ; Ferredoxin-NADP Reductase/chemistry/*metabolism ; Ferredoxins/chemistry/*metabolism ; Leptospira interrogans/*enzymology ; Models, Molecular ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; Sequence Alignment ; },
abstract = {BACKGROUND: Ferredoxins are small iron-sulfur proteins that participate as electron donors in various metabolic pathways. They are recognized substrates of ferredoxin-NADP+ reductases (FNR) in redox metabolisms in mitochondria, plastids, and bacteria. We previously found a plastidic-type FNR in Leptospira interrogans (LepFNR), a parasitic bacterium of animals and humans. Nevertheless, we did not identify plant-type ferredoxins or flavodoxins, the common partners of this kind of FNR.

METHODS: Sequence alignment, phylogenetical analyses and structural modeling were performed for the identification of a 2[4Fe4S] ferredoxin (LepFd2) as a putative redox partner of LepFNR in L. interrogans. The gene encoding LepFd2 was cloned and the protein overexpressed and purified. The functional properties of LepFd2 and LepFNR-LepFd2 complex were analyzed by kinetic and mutagenesis studies.

RESULTS: We succeeded in expressing and purifying LepFd2 with its FeS cluster properly bound. We found that LepFd2 exchanges electrons with LepFNR. Moreover, a unique structural subdomain of LepFNR (loop P75-Y91), was shown to be involved in the recognition and binding of LepFd2. This structural subdomain is not found in other FNR homologs.

CONCLUSIONS: We report for the first time a redox pair in L. interrogans in which a plastidic FNR exchanges electron with a bacterial 2[4Fe4S] ferredoxin. We characterized this reaction and proposed a model for the productive LepFNR-LepFd2 complex.

GENERAL SIGNIFICANCE: Our findings suggest that the interaction of LepFNR with the iron-sulfur protein would be different from the one previously described for the homolog enzymes. This knowledge would be useful for the design of specific LepFNR inhibitors.},
}

Amino Acid Sequence
Ferredoxin-NADP Reductase/chemistry/*metabolism
Ferredoxins/chemistry/*metabolism
Leptospira interrogans/*enzymology
Models, Molecular
Oxidation-Reduction
Phylogeny
Protein Conformation
Sequence Alignment

@article {pmid31786061,
year = {2019},
author = {Chiang, AC and McCartney, E and O'Farrell, PH and Ma, H},
title = {A Genome-wide Screen Reveals that Reducing Mitochondrial DNA Polymerase Can Promote Elimination of Deleterious Mitochondrial Mutations.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2019.10.060},
pmid = {31786061},
issn = {1879-0445},
abstract = {A mutant mitochondrial genome arising amid the pool of mitochondrial genomes within a cell must compete with existing genomes to survive to the next generation. Even weak selective forces can bias transmission of one genome over another to affect the inheritance of mitochondrial diseases and guide the evolution of mitochondrial DNA (mtDNA). Studies in several systems suggested that purifying selection in the female germline reduces transmission of detrimental mitochondrial mutations [1-7]. In contrast, some selfish genomes can take over despite a cost to host fitness [8-13]. Within individuals, the outcome of competition is therefore influenced by multiple selective forces. The nuclear genome, which encodes most proteins within mitochondria, and all external regulators of mitochondrial biogenesis and dynamics can influence the competition between mitochondrial genomes [14-18], yet little is known about how this works. Previously, we established a Drosophila line transmitting two mitochondrial genomes in a stable ratio enforced by purifying selection benefiting one genome and a selfish advantage favoring the other [8]. Here, to find nuclear genes that impact mtDNA competition, we screened heterozygous deletions tiling ∼70% of the euchromatic regions and examined their influence on this ratio. This genome-wide screen detected many nuclear modifiers of this ratio and identified one as the catalytic subunit of mtDNA polymerase gene (POLG), tam. A reduced dose of tam drove elimination of defective mitochondrial genomes. This study suggests that our approach will uncover targets for interventions that would block propagation of pathogenic mitochondrial mutations.},
}

@article {pmid31784872,
year = {2019},
author = {Wang, J and Yang, M and Xiao, H and Huang, GH and Deng, F and Hu, Z},
title = {Genome Analysis of Dasineura jujubifolia Toursvirus 2, A Novel Ascovirus.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12250-019-00177-2},
pmid = {31784872},
issn = {1995-820X},
abstract = {So far, ascoviruses have only been identified from Lepidoptera host insects and their transmission vectors-endoparasitic wasps. Here, we reported the first finding of a complete novel ascovirus genome from a Diptera insect, Dasineura jujubifolia. Initially, sequence fragments with homology to ascoviruses were incidentally identified during metagenomic sequencing of the mitochondria of D. jujubifolia (Cecidomyiidae, Diptera) which is a major pest on Ziziphus jujuba. Then a full circular viral genome was assembled from the metagenomic data, which has an A+T percentage of 74% and contains 142,600 bp with 141 open reading frames (ORFs). Among the 141 ORFs, 37 were conserved in all sequenced ascoviruses (core genes) including proteins predicted to participate in DNA replication, gene transcription, protein modification, virus assembly, lipid metabolism and apoptosis. Multi-gene families including those encode for baculovirus repeated open reading frames (BROs), myristylated membrane proteins, RING/U-box E3 ubiquitin ligases, and ATP-binding cassette (ABC) transporters were found in the virus genome. Phylogenetic analysis showed that the newly identified virus belongs to genus Toursvirus of Ascoviridae, and is therefore named as Dasineura jujubifolia toursvirus 2 (DjTV-2a). The virus becomes the second reported species of the genus after Diadromus pulchellus toursvirus 1 (DpTV-1a). The genome arrangement of DjTV-2a is quite different from that of DpTV-1a, suggesting these two viruses separated in an early time of evolution. The results suggest that the ascoviruses may infect a much broader range of hosts than our previous knowledge, and shed lights on the evolution of ascoviruses and particularly on that of the toursviruses.},
}

@article {pmid31780199,
year = {2019},
author = {Waltz, F and Giegé, P},
title = {Striking Diversity of Mitochondria-Specific Translation Processes across Eukaryotes.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2019.10.004},
pmid = {31780199},
issn = {0968-0004},
abstract = {Mitochondria are essential organelles that act as energy conversion powerhouses and metabolic hubs. Their gene expression machineries combine traits inherited from prokaryote ancestors and specific features acquired during eukaryote evolution. Mitochondrial research has wide implications ranging from human health to agronomy. We highlight recent advances in mitochondrial translation. Functional, biochemical, and structural data have revealed an unexpected diversity of mitochondrial translation systems, particularly of their key players, the mitochondrial ribosomes (mitoribosomes). Ribosome assembly and translation mechanisms, such as initiation, are discussed and put in perspective with the prevalence of eukaryote-specific families of mitochondrial translation factors such as pentatricopeptide repeat (PPR) proteins.},
}

@article {pmid31300133,
year = {2019},
author = {Mirbadie, SR and Najafi Nasab, A and Mohaghegh, MA and Norouzi, P and Mirzaii, M and Spotin, A},
title = {Molecular phylodiagnosis of Echinococcus granulosus sensu lato and Taenia hydatigena determined by mitochondrial Cox1 and SSU-rDNA markers in Iranian dogs: Indicating the first record of pig strain (G7) in definitive host in the Middle East.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {65},
number = {},
pages = {88-95},
doi = {10.1016/j.cimid.2019.05.005},
pmid = {31300133},
issn = {1878-1667},
mesh = {Animals ; Cyclooxygenase 1/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/diagnosis/*epidemiology ; Dogs/parasitology ; Echinococcosis/diagnosis/epidemiology/*veterinary ; Echinococcus granulosus/genetics ; Feces/parasitology ; Genotype ; Intestinal Diseases, Parasitic/diagnosis/*veterinary ; Iran/epidemiology ; Middle East/epidemiology ; Mitochondria/genetics ; *Phylogeny ; Prevalence ; Swine/parasitology ; Taenia/genetics ; Taeniasis/diagnosis/epidemiology/*veterinary ; },
abstract = {Unawareness of canine parasitic diseases among at-risk hosts and an uncontrolled program of stray dog population have caused that zoonotic parasites received great attention in endemic regions of the Middle East. A total of 552 faecal samples were collected between December 2016 to January 2018 from stray (n = 408) and domestic (n = 144) dogs of Iran. All specimens were coproscopically observed following concentration and flotation techniques. Subsequently, the DNAs of taeniid eggs were extracted, amplified, and sequenced by targeting of mitochondrial cytochrome oxidase subunit 1 and small-subunit ribosomal DNA markers. The overall prevalence of canine intestinal parasites found 53.6%. The following parasites and their total frequencies were identified: taeniid (10.5%), Dicrocoelium dendriticum (0.7%), Trichuris vulpis (1.2%), Capillaria spp. (2.3%), Blastocystis spp. (5.2%), Ancylostoma spp. (2%), Eimeria spp. (13.2%), Dipylidium caninum (2.3%), Toxocara canis (3.8%), Giardia spp. (8.5%), and Toxascaris leonina (3.6%). Stray dogs were characterized more likely to be poliparasitized and indicated a higher prevalence of taeniid (10.9%), T. canis (4.4%) Giardia spp. (10.1%) than domestic dogs (P > 0.05). Phylogenetic and sequence analysis of Cox1 and SSU-rDNA indicated a low genetic diversity (Haplotype diversity; 0 to 0.495) in E. granulosus sensu lato G1, G3, G7 genotypes, and Taenia hydatigena. The pairwise sequence distances between G7 isolates showed an intra-diversity of 0.7%-1.5% and identity of 98.5%-100%. The first occurrence of pig strain (G7) from Iranian dogs might have substantial implications in the drug treatment of infected dogs due to the shorter maturation time of G7 compared with G1 genotype. Thus, the preventive strategies should be noticed to determine the risk factors, the importance of applying the hygienic practices, and well adjusting deworming programs for the Iranian dogs and at-risk individuals.},
}

Animals
Cyclooxygenase 1/genetics
DNA, Ribosomal/genetics
Dog Diseases/diagnosis/*epidemiology
Dogs/parasitology
Echinococcosis/diagnosis/epidemiology/*veterinary
Echinococcus granulosus/genetics
Feces/parasitology
Genotype
Intestinal Diseases, Parasitic/diagnosis/*veterinary
Iran/epidemiology
Middle East/epidemiology
Mitochondria/genetics
*Phylogeny
Prevalence
Swine/parasitology
Taenia/genetics
Taeniasis/diagnosis/epidemiology/*veterinary

@article {pmid31136801,
year = {2019},
author = {Peres, EA and Benedetti, AR and Hiruma, ST and Sobral-Souza, T and Pinto-da-Rocha, R},
title = {Phylogeography of Sodreaninae harvestmen (Arachnida: Opiliones: Gonyleptidae): Insights into the biogeography of the southern Brazilian Atlantic Forest.},
journal = {Molecular phylogenetics and evolution},
volume = {138},
number = {},
pages = {1-16},
doi = {10.1016/j.ympev.2019.05.028},
pmid = {31136801},
issn = {1095-9513},
mesh = {Animals ; Arachnida/*classification/genetics ; Bayes Theorem ; Brazil ; Cell Nucleus/genetics ; *Forests ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Population Dynamics ; },
abstract = {The Brazilian Atlantic Forest has long been considered a global biodiversity hotspot. In the last decade, the phylogeographic patterns of endemic taxa have been unraveling the biogeographic history of the biome. However, highly diverse invertebrate species have still been poorly studied. Sodreana harvestmen (Gonyleptidae) are distributed in most of the humid coastal forests in the southern portion of the Atlantic Forest, a region that has experienced complex topographic evolution and differing climatic conditions since the Early Cretaceous, which likely affected the geographic distribution and diversification of the group. In this study, we investigated the molecular phylogeny and phylogeography of Sodreana to clarify the species relationships and to make inferences about the historical biogeography of the southern Atlantic Forest. We applied coalescent-based phylogenetic analyses using one mitochondrial and three nuclear markers coupled with an ecological niche modeling approach to verify relationships among species, date the main divergence events in the genus, and make inferences concerning possible changes in the geographical distribution and population dynamics from the past. Our results supported the validity of most Sodreana species and suggested that Paleogene-Neogene geomorphologic processes such as the formation of rivers systems, uplift of mountain ranges and related environmental changes have profoundly affected the evolutionary history of Sodreana. The ecological niche models showed that the areas potentially occupied by the species were greatly reduced during Quaternary glacial periods but no recent lineage divergences or genetic bottlenecks were detected, suggesting that climatically stable micro-habitats could have helped maintain populations during drier periods. Our study highlights the importance of humidity-dependent and poor-dispersal taxa in understanding the effects of ancient geological and climate processes on the Atlantic Forest biota.},
}

Animals
Arachnida/*classification/genetics
Bayes Theorem
Brazil
Cell Nucleus/genetics
*Forests
Genetic Variation
Genetics, Population
Haplotypes/genetics
Mitochondria/genetics
Phylogeny
*Phylogeography
Population Dynamics

@article {pmid31121309,
year = {2019},
author = {Santos, JCMD and Ferreira, ES and Oliveira, C and Oliveira, TB and Costa, ASLD and Queiroz, AKO and Schneider, H and Sampaio, I and Santos, S},
title = {Phylogeny of the genus Hypophthalmus Cuvier, 1829 (Pimelodidae - Siluriformes), based on a multilocus analysis, indicates diversification and introgression in the Amazon basin.},
journal = {Molecular phylogenetics and evolution},
volume = {137},
number = {},
pages = {285-292},
doi = {10.1016/j.ympev.2019.05.017},
pmid = {31121309},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genetic Loci ; *Genetic Variation ; Hybridization, Genetic ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; },
abstract = {The genus Hypophthalmus encompasses four valid South American freshwater catfish species: H. marginatus, H. edentatus, H. fimbriatus, and H. oremaculatus. More recently two new species were proposed Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2. While Hypophthalmus species are a fundamentally important resource for the commercial fisheries that operate in the continental waters of the Amazon basin, their phylogenetic relationships and the true diversity of the genus have yet to be defined conclusively. Given this, the present study analyzed sequences of the mitochondrial COI gene and four nuclear markers (RAG2, Myh6, Plagl2 and Glyt) to evaluate the phylogenetic relationships and the diversity of the species of this genus. All the analyses showed that Hypophthalmus is monophyletic, and the species delimitation tests recovered all the Hypophthalmus taxa as distinct species. The putative new species Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2 presented mean genetic divergence similar to or greater than that observed between valid Hypophthalmus taxa. All the analyses showed that H. oremaculatus is the sister group of H. n. sp. 1, which together group with H. fimbriatus. This clade is the sister group of the clade containing H. edentatus and H. n. sp. 2. One specimen, morphologically identified as H. oremaculatus, presented the nuclear genome of this species and the mitochondrial genome of H. n. sp. 1; while another specimen, morphologically identified as H. n. sp. 2, presented the nuclear Myh6 of H. n. sp. 2 and the mitochondrial and RAG2 genome of H. edentatus. These results indicate that hybridization and introgression has occurred between species in Hypophthalmus. The findings of this study indicate that the diversity of the Hypophthalmus is underestimated, emphasize the need for a taxonomic review of the genus, and a more systematic evaluation of the hybridization patterns found, to understanding the role of hybridization and introgression in the evolution of the genus.},
}

Animals
Bayes Theorem
Catfishes/*classification/*genetics
Cell Nucleus/genetics
DNA, Mitochondrial/genetics
*Genetic Loci
*Genetic Variation
Hybridization, Genetic
Mitochondria/genetics
*Phylogeny
Species Specificity

@article {pmid31112782,
year = {2019},
author = {Gandini, CL and Garcia, LE and Abbona, CC and Sanchez-Puerta, MV},
title = {The complete organelle genomes of Physochlaina orientalis: Insights into short sequence repeats across seed plant mitochondrial genomes.},
journal = {Molecular phylogenetics and evolution},
volume = {137},
number = {},
pages = {274-284},
doi = {10.1016/j.ympev.2019.05.012},
pmid = {31112782},
issn = {1095-9513},
mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; Genome, Plastid ; Introns/genetics ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Seeds/*genetics ; Solanaceae/*genetics ; },
abstract = {Short repeats (SR) play an important role in shaping seed plant mitochondrial genomes (mtDNAs). However, their origin, distribution, and relationships across the different plant lineages remain unresolved. We focus on the angiosperm family Solanaceae that shows great variation in repeat content and extend the study to a wide diversity of seed plants. We determined the complete nucleotide sequences of the organellar genomes of the medicinal plant Physochlaina orientalis (Solanaceae), member of the tribe Hyoscyameae. To understand the evolution of the P. orientalis mtDNA we made comparisons with those of five other Solanaceae. P. orientalis mtDNA presents the largest mitogenome (∼685 kb in size) among the Solanaceae and has an unprecedented 8-copy repeat family of ∼8.2 kb in length and a great number of SR arranged in tandem-like structures. We found that the SR in the Solanaceae share a common origin, but these only expanded in members of the tribe Hyoscyameae. We discuss a mechanism that could explain SR formation and expansion in P. orientalis and Hyoscyamus niger. Finally, the great increase in plant mitochondrial data allowed us to systematically extend our repeat analysis to a total of 136 seed plants to characterize and analyze for the first time families of SR among seed plant mtDNAs.},
}

Base Sequence
DNA, Mitochondrial/genetics
*Genome, Mitochondrial
*Genome, Plant
Genome, Plastid
Introns/genetics
Microsatellite Repeats/*genetics
Mitochondria/genetics
Phylogeny
Seeds/*genetics
Solanaceae/*genetics

@article {pmid31018163,
year = {2019},
author = {Torres-Cambas, Y and Ferreira, S and Cordero-Rivera, A and Lorenzo-Carballa, MO},
title = {Mechanisms of allopatric speciation in an Antillean damselfly genus (Odonata, Zygoptera): Vicariance or long-distance dispersal?.},
journal = {Molecular phylogenetics and evolution},
volume = {137},
number = {},
pages = {14-21},
doi = {10.1016/j.ympev.2019.04.018},
pmid = {31018163},
issn = {1095-9513},
mesh = {Animal Migration/*physiology ; Animals ; Base Sequence ; Cell Nucleus/genetics ; Cuba ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; Genetic Variation ; Mitochondria/genetics ; Odonata/*genetics/*physiology ; Phylogeny ; Species Specificity ; Time Factors ; },
abstract = {We have examined divergence times of the Antillean damselfly genus Hypolestes, to elucidate which mechanism of allopatric speciation, vicariance or long-distance dispersal, could better explain the currently observed disjunct distributions of this genus. Samples of the three extant species of the genus, Hypolestes clara (Jamaica), H. hatuey (Hispaniola) and H. trinitatis (Cuba), were collected. Mitochondrial and nuclear DNA gene fragments were amplified to reconstruct phylogenetic relationships and estimate divergence times in this genus. Hypolestes comprises currently three species, which consist in four geographically and genetically isolated lineages located in Jamaica, Hispaniola, Eastern Cuba and Central Cuba. Results of our analyses suggest that the three species diverged between ∼5.91 and 1.69 mya, and that the separation between the lineages from Central Cuba and Eastern Cuba occurred between ∼2.0 and 0.62 mya. Disjunct distributions in the genus Hypolestes can be better explained by a long-distance dispersal mechanism, since the divergence times of the three species do not coincide with the timeline formation of the geographic barriers between Cuba, Hispaniola and Jamaica. The Cuban lineages of H. trinitatis constitute different molecular operational taxonomic units (MOTU). The elevation of these MOTU to the species category requires the analysis of additional characters.},
}

Animal Migration/*physiology
Animals
Base Sequence
Cell Nucleus/genetics
Cuba
DNA, Mitochondrial/genetics
*Genetic Speciation
Genetic Variation
Mitochondria/genetics
Odonata/*genetics/*physiology
Phylogeny
Species Specificity
Time Factors

@article {pmid30974201,
year = {2019},
author = {Strong, EE and Whelan, NV},
title = {Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda).},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {87-103},
doi = {10.1016/j.ympev.2019.04.009},
pmid = {30974201},
issn = {1095-9513},
mesh = {Algorithms ; Animal Shells/anatomy & histology ; Animals ; Bayes Theorem ; California ; Cell Nucleus/genetics ; Gastropoda/anatomy & histology/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. We assembled a multilocus mitochondrial (COI, 16S) and nuclear gene (ITS1) dataset for ∼100 populations collected across the range of the genus. We generated primary species hypotheses using ABGD with best-fit model-corrected distances and further explored our data, both individual gene partitions and concatenated datasets, using a diversity of phylogenetic and species delimitation methods (Bayesian inference, maximum likelihood estimation, StarBEAST2, bGMYC, bPTP, BP&P). Our secondary species delimitation hypotheses, based primarily on the criterion of reciprocal monophyly, and informed by a combination of geography and morphology, support the interpretation that Juga comprises a mixture of geographically widespread species and narrow range endemics. As might be expected in taxa with low vagility and poor dispersal capacities, analysis of molecular variance (AMOVA) revealed highly structured populations with up to 80% of the observed genetic variance explained by variation between populations. Analyses with bGMYC, bPTP, and BP&P appeared sensitive to this genetic structure and returned highly dissected species hypotheses that are likely oversplit. The species diversity of Juga is concluded to be lower than presently recognized, and the systematics to require extensive revision. Features of the teleoconch considered significant in species-level and subgeneric classification were found to be variable within some species, sometimes at a single site. Of a number of potentially new species identified in non-peer reviewed reports and field guides, only one was supported as a distinct OTU.},
}

Algorithms
Animal Shells/anatomy & histology
Animals
Bayes Theorem
California
Cell Nucleus/genetics
Gastropoda/anatomy & histology/*genetics
*Genetic Variation
Genetics, Population
Geography
Haplotypes/genetics
Mitochondria/genetics
Phylogeny
Species Specificity

@article {pmid30954588,
year = {2019},
author = {Sajeela, KA and Gopalakrishnan, A and Basheer, VS and Mandal, A and Bineesh, KK and Grinson, G and Gopakumar, SD},
title = {New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean.},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {53-64},
doi = {10.1016/j.ympev.2019.04.007},
pmid = {30954588},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Indian Ocean ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Penaeidae/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.},
}

Animals
Base Sequence
Bayes Theorem
Cell Nucleus/*genetics
Electron Transport Complex IV/genetics
Genetic Markers
*Genetic Variation
Genetics, Population
Geography
Haplotypes/genetics
Indian Ocean
Microsatellite Repeats/genetics
Mitochondria/*genetics
Penaeidae/*genetics
Phylogeny
Species Specificity

@article {pmid30951923,
year = {2019},
author = {Kinoshita, G and Nunome, M and Kryukov, AP and Kartavtseva, IV and Han, SH and Yamada, F and Suzuki, H},
title = {Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus).},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {65-75},
doi = {10.1016/j.ympev.2019.04.003},
pmid = {30951923},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/genetics ; DNA/genetics ; DNA, Mitochondrial/genetics ; Far East ; Genetic Loci ; Geography ; Hares/classification/*genetics ; *Islands ; Mitochondria/*genetics ; Phylogeny ; *Phylogeography ; },
abstract = {Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.},
}

Animals
Base Sequence
Bayes Theorem
Cell Nucleus/genetics
DNA/genetics
DNA, Mitochondrial/genetics
Far East
Genetic Loci
Geography
Hares/classification/*genetics
*Islands
Mitochondria/*genetics
Phylogeny
*Phylogeography

@article {pmid29938587,
year = {2019},
author = {Gvozdanović, K and Margeta, V and Margeta, P and Djurkin Kušec, I and Galović, D and Dovč, P and Kušec, G},
title = {Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism.},
journal = {Animal biotechnology},
volume = {30},
number = {3},
pages = {242-251},
doi = {10.1080/10495398.2018.1478847},
pmid = {29938587},
issn = {1532-2378},
mesh = {Animals ; Breeding ; DNA, Mitochondrial/genetics ; Female ; Gene Frequency ; *Genetic Variation ; Haplotypes ; Male ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Sus scrofa ; Swine/*genetics ; },
abstract = {The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.},
}

Animals
Breeding
DNA, Mitochondrial/genetics
Female
Gene Frequency
*Genetic Variation
Haplotypes
Male
Microsatellite Repeats/*genetics
Mitochondria/genetics
Phylogeny
Polymorphism, Genetic
Sus scrofa
Swine/*genetics

@article {pmid31216623,
year = {2019},
author = {Myszczyński, K and Ślipiko, M and Sawicki, J},
title = {Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends.},
journal = {International journal of molecular sciences},
volume = {20},
number = {12},
pages = {},
doi = {10.3390/ijms20122963},
pmid = {31216623},
issn = {1422-0067},
support = {Grant No. 2017/01/X/NZ8/01094, Grant No. 2016/21/B/NZ8/03325, Grant No. 2015/19/B/NZ8/03970//Narodowe Centrum Nauki/ ; },
mesh = {Base Composition ; Bryophyta/classification/genetics ; Embryophyta/*classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Genomics/methods ; Open Reading Frames ; Phylogeny ; *RNA Editing ; RNA, Messenger/*genetics ; *RNA, Plant ; },
abstract = {RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.},
}

Base Composition
Bryophyta/classification/genetics
Embryophyta/*classification/*genetics
Genome Size
*Genome, Mitochondrial
Genomics/methods
Open Reading Frames
Phylogeny
*RNA Editing
RNA, Messenger/*genetics
*RNA, Plant

@article {pmid30395997,
year = {2019},
author = {López-Rubio, A and Suaza-Vasco, JD and Solari, S and Gutiérez-Builes, L and Porter, C and Uribe, SI},
title = {Intraspecific phylogeny of Anopheles (Kerteszia) neivai Howard, Dyar & Knab 1913, based on mitochondrial and nuclear ribosomal genes.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {67},
number = {},
pages = {183-190},
doi = {10.1016/j.meegid.2018.10.013},
pmid = {30395997},
issn = {1567-7257},
mesh = {Animals ; Anopheles/*classification/*genetics ; Central America/epidemiology ; *Genes, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/*genetics ; South America/epidemiology ; },
abstract = {Three mitochondrial regions and a fragment of a large nuclear ribosomal subunit was used to study the evolutionary patterns of An. neivai, a mosquito inhabiting mangroves and tropical forest in the lowland and coastal areas of the Yucatan Peninsula through the Pacific Ecuadorian coast. This species exhibits epidemiological importance regarding Malaria transmission in natural ecosystems, particularly in rural areas of the Pacific Colombian coast. The results based on phylogenetic networks and Bayesian inference showed no robust evidence supporting the existence of previously suggested cryptic species. Diversification patterns in geographically widespread species such as this one, are complex and therefore could impact malaria control strategies. Further studies focused on behavior, morphology, and phylogenomics will improve the understanding of the evolutionary patterns within An. neivai and its role as a disease vector.},
}

Animals
Anopheles/*classification/*genetics
Central America/epidemiology
*Genes, Mitochondrial
Haplotypes
Mitochondria/*genetics
Phylogeny
RNA, Ribosomal/*genetics
South America/epidemiology

@article {pmid31766564,
year = {2019},
author = {Brieba, LG},
title = {Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System.},
journal = {Plants (Basel, Switzerland)},
volume = {8},
number = {12},
pages = {},
doi = {10.3390/plants8120533},
pmid = {31766564},
issn = {2223-7747},
support = {13//SEP-Cinvestav/ ; },
abstract = {Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.},
}

@article {pmid31754022,
year = {2019},
author = {Li, H and Rukina, D and David, FPA and Li, TY and Oh, CM and Gao, AW and Katsyuba, E and Bou Sleiman, M and Komljenovic, A and Huang, Q and Williams, RW and Robinson-Rechavi, M and Schoonjans, K and Morgenthaler, S and Auwerx, J},
title = {Identifying gene function and module connections by the integration of multispecies expression compendia.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.251983.119},
pmid = {31754022},
issn = {1549-5469},
abstract = {The functions of many eukaryotic genes are still poorly understood. Here, we developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Module Association Determination (G-MAD) allows the annotation of gene function. Second, Module-Module Association Determination (M-MAD) allows predicting connectivity among modules. We applied the GeneBridge tools to large-scale multispecies expression compendia-1700 data sets with over 300,000 samples from human, mouse, rat, fly, worm, and yeast-collected in this study. G-MAD identifies novel functions of genes-for example, DDT in mitochondrial respiration and WDFY4 in T cell activation-and also suggests novel components for modules, such as for cholesterol biosynthesis. By applying G-MAD on data sets from respective tissues, tissue-specific functions of genes were identified-for instance, the roles of EHHADH in liver and kidney, as well as SLC6A1 in brain and liver. Using M-MAD, we identified a list of module-module associations, such as those between mitochondria and proteasome, mitochondria and histone demethylation, as well as ribosomes and lipid biosynthesis. The GeneBridge tools together with the expression compendia are available as an open resource, which will facilitate the identification of connections linking genes, modules, phenotypes, and diseases.},
}

@article {pmid31751405,
year = {2019},
author = {Voleman, L and Doležal, P},
title = {Mitochondrial dynamics in parasitic protists.},
journal = {PLoS pathogens},
volume = {15},
number = {11},
pages = {e1008008},
doi = {10.1371/journal.ppat.1008008},
pmid = {31751405},
issn = {1553-7374},
abstract = {The shape and number of mitochondria respond to the metabolic needs during the cell cycle of the eukaryotic cell. In the best-studied model systems of animals and fungi, the cells contain many mitochondria, each carrying its own nucleoid. The organelles, however, mostly exist as a dynamic network, which undergoes constant cycles of division and fusion. These mitochondrial dynamics are driven by intricate protein machineries centered around dynamin-related proteins (DRPs). Here, we review recent advances on the dynamics of mitochondria and mitochondrion-related organelles (MROs) of parasitic protists. In contrast to animals and fungi, many parasitic protists from groups of Apicomplexa or Kinetoplastida carry only a single mitochondrion with a single nucleoid. In these groups, mitochondrial division is strictly coupled to the cell cycle, and the morphology of the organelle responds to the cell differentiation during the parasite life cycle. On the other hand, anaerobic parasitic protists such as Giardia, Entamoeba, and Trichomonas contain multiple MROs that have lost their organellar genomes. We discuss the function of DRPs, the occurrence of mitochondrial fusion, and mitophagy in the parasitic protists from the perspective of eukaryote evolution.},
}

@article {pmid31750917,
year = {2019},
author = {Costello, R and Emms, DM and Kelly, S},
title = {Gene duplication accelerates the pace of protein gain and loss from plant organelles.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz275},
pmid = {31750917},
issn = {1537-1719},
abstract = {Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the plant kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrated that change to organellar targeting is associated with an increase in the rate of molecular sequence evolution and that changes in protein targeting predominantly occurred in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein targeting occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.},
}

@article {pmid31740334,
year = {2019},
author = {Feng, JM and Jiang, CQ and Sun, ZY and Hua, CJ and Wen, JF and Miao, W and Xiong, J},
title = {Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106687},
doi = {10.1016/j.ympev.2019.106687},
pmid = {31740334},
issn = {1095-9513},
abstract = {Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.},
}

@article {pmid31716895,
year = {2019},
author = {Tominaga, A and Matsui, M and Tanabe, S and Nishikawa, K},
title = {A revision of Hynobius stejnegeri, a lotic breeding salamander from western Japan, with a description of three new species (Amphibia, Caudata, Hynobiidae).},
journal = {Zootaxa},
volume = {4651},
number = {3},
pages = {zootaxa.4651.3.1},
doi = {10.11646/zootaxa.4651.3.1},
pmid = {31716895},
issn = {1175-5334},
mesh = {Animals ; Breeding ; Japan ; Mitochondria ; Phylogeny ; Tooth ; *Urodela ; },
abstract = {A lotic-breeding salamander Hynobius stejnegeri, formerly called H. yatsui, from western Japan is revised based on genetic and morphological evidence, and three species are described: H. guttatus sp. nov. from Chubu-Kinki districts of Honshu Island, H. tsurugiensis sp. nov. from east highland of Shikoku Island, and H. kuishiensis sp. nov. from other parts of Shikoku Island. Thus, H. stejnegeri sensu stricto is restricted to Kyushu Island. Of these four species, H. kuishiensis sp. nov. contains two distinct mitochondrial lineages, but this split is not reflected in differentiation of allozyme (nuclear genome) markers. These species are morphologically similar to each other but can be differentiated by several characteristics, especially in combination of dorsal coloration, the number of vomerine, upper, and lower jaw teeth, and depth of vomerine teeth series. In coloration, H. guttatus sp. nov. is brown or dark brown mostly with tiny white to brownish white marking, while H. tsurugiensis sp. nov. is dark brown with bright yellow continuous markings. Hynobius kuishiensis sp. nov. is reddish purple or dark brown with small to continuous brownish white markings, in contrast to reddish purple or dark brown with small to large brownish white markings in H. stejnegeri.},
}

Animals
Breeding
Japan
Mitochondria
Phylogeny
Tooth
*Urodela

@article {pmid31716534,
year = {2019},
author = {Braun, MP and Datzmann, T and Arndt, T and Reinschmidt, M and Schnitker, H and Bahr, N and Sauer-Gürth, H and Wink, M},
title = {A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, †Mascarinus) with taxonomic implications.},
journal = {Zootaxa},
volume = {4563},
number = {3},
pages = {zootaxa.4563.3.8},
doi = {10.11646/zootaxa.4563.3.8},
pmid = {31716534},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; Mitochondria ; *Parrots ; Phylogeny ; *Psittaciformes ; *Psittacula ; },
abstract = {The long-tailed parakeets of the genus Psittacula Cuvier, 1800 have thus far been regarded as a homogeneous and monophyletic group of parrots. We used nucleotide sequences of two genetic markers (mitochondrial CYTB, nuclear RAG-1) to reconstruct the phylogenetic relationships of Psittacula and closely related species. We found that the Asian genus Psittacula is apparently paraphyletic because two genera of short-tailed parrots, Psittinus Blyth, 1842 and Tanygnathus Wagler, 1832, cluster within Psittacula, as does †Mascarinus Lesson, 1830. To create monophyletic genera, we propose recognition of the following genera: Himalayapsitta Braun, 2016 for P. himalayana, P. finschii, P. roseata, and P. cyanocephala; Nicopsitta Braun, 2016 for P. columboides and P. calthrapae; Belocercus S. Müller, 1847 for P. longicauda; Psittacula Cuvier, 1800 for P. alexandri and P. derbiana; Palaeornis Vigors, 1825 for †P. wardi and P. eupatria; and Alexandrinus Braun, 2016 for P. krameri, †P. exsul, and P. (eques) echo. Additionally, Psittacula krameri and P. alexandri are paraphyletic species, which should be split to form monophyletic species.},
}

Animals
Base Sequence
Mitochondria
*Parrots
Phylogeny
*Psittaciformes
*Psittacula

@article {pmid31716329,
year = {2019},
author = {Macià, R and Mally, R and Ylla, J and Gastón, J and Huertas, M},
title = {Integrative revision of the Iberian species of Coscinia Hübner, [1819] sensu lato and Spiris Hübner, [1819], (Lepidoptera: Erebidae, Arctiinae).},
journal = {Zootaxa},
volume = {4615},
number = {3},
pages = {zootaxa.4615.3.1},
doi = {10.11646/zootaxa.4615.3.1},
pmid = {31716329},
issn = {1175-5334},
mesh = {Animals ; Female ; Genitalia ; Male ; Mitochondria ; *Moths ; *Mustelidae ; Phylogeny ; },
abstract = {The Iberian species of the genera Coscinia Hübner, [1819] and Spiris Hübner, [1819], as well as three other species from the Mediterranean area, are revised based on morphological and molecular genetic data. Our results suggest the separation into four morphologically and phylogenetically different genera: Coscinia Hübner, [1819], Lerautia Kemal Koçak, 2006 stat. rev., Sagarriella Macià, Mally, Ylla, Gastón Huertas gen. nov. and Spiris Hübner, [1819]. We conclude that there are eight species of the Coscinia genus group present in the studied area: Coscinia cribraria (Linnaeus, 1758), Coscinia chrysocephala (Hübner, [1810]) stat. rev., Coscinia mariarosae Expósito, 1991, Sagarriella libyssa caligans (Turati, 1907) comb. nov., Sagarriella romei (Sagarra, 1924) (= romeii sensu auctorum) comb. nov., Spiris striata Hübner, [1819], Spiris slovenica (Daniel, 1939) and Lerautia bifasciata (Rambur, 1832) comb. rev. We consider Coscinia cribraria benderi (Marten, 1957) stat. nov., Coscinia c. rippertii (Boisduval, 1834) and Coscinia c. ibicenca Kobes, 1991 stat. rev. to be subspecies of C. cribraria. COI Barcodes of C. cribraria diverge by up to 7.99%, and the investigated specimens group into six different COI Barcode BINs. Both the phylogenetic analysis of mitochondrial and nuclear DNA and the morphological examination of different specimens corroborate the changes in taxonomic status and justify the proposed taxonomic categories. We present images of adults and genitalia of both sexes, the immature stages of some of the species and the subspecies studied, as well as phylogenetic results from the analysis of genetic data. We also include data on life history, foodplants and geographical distribution.},
}

Animals
Female
Genitalia
Male
Mitochondria
*Moths
*Mustelidae
Phylogeny

@article {pmid31716318,
year = {2019},
author = {Hibbitts, TJ and Ryberg, WA and Harvey, JA and Voelker, G and Lawing, AM and Adams, CS and Neuharth, DB and Dittmer, DE and Duran, CM and Wolaver, BD and Pierre, JP and Labay, BJ and Laduc, TJ},
title = {Phylogenetic structure of Holbrookia lacerata (Cope 1880) (Squamata: Phrynosomatidae): one species or two?.},
journal = {Zootaxa},
volume = {4619},
number = {1},
pages = {zootaxa.4619.1.6},
doi = {10.11646/zootaxa.4619.1.6},
pmid = {31716318},
issn = {1175-5334},
mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial ; *Lizards ; Mitochondria ; Phylogeny ; Texas ; },
abstract = {Species delimitation attempts to match species-level taxonomy with actual evolutionary lineages. Such taxonomic conclusions are typically, but not always, based on patterns of congruence across multiple data sources and methods of analyses. Here, we use this pluralistic approach to species delimitation to help resolve uncertainty in species boundaries of phrynosomatid sand lizards of the genus Holbrookia. Specifically, the Spot-tailed Earless Lizard (H. lacerata) was historically divided into a northern (H. l. lacerata) and southern (H. l. subcaudalis) subspecies based on differences in morphology and allopatry, but no research has been conducted evaluating genetic differences between these taxa. In this study, patterns in sequence data derived from two genes, one nuclear and one mitochondrial, for 66 individuals sampled across 18 counties in Texas revealed three strongly supported, reciprocally monophyletic lineages, each comprised of individuals from a single geographic region. Distinct genetic variation evident across two of these regions corresponds with differences in morphology, differences in environmental niche, and lines up with the presumed geographic barrier, the Balcones Escarpment, which is the historical subspecies boundary. The combined evidence from genetics, morphology and environmental niche is sufficient to consider these subspecies as distinct species with the lizards north of the Balcones Escarpment retaining the name Holbrookia lacerata, and those south of the Balcones Escarpment being designated as Holbrookia subcaudalis.},
}

Animals
Biological Evolution
DNA, Mitochondrial
*Lizards
Mitochondria
Phylogeny
Texas

@article {pmid31715832,
year = {2019},
author = {Han, H and Skou, P and Cheng, R},
title = {Neochloroglyphica, a new genus of Geometrinae from China (Lepidoptera, Geometridae), with description of a new species.},
journal = {Zootaxa},
volume = {4571},
number = {1},
pages = {zootaxa.4571.1.6},
doi = {10.11646/zootaxa.4571.1.6},
pmid = {31715832},
issn = {1175-5334},
mesh = {Animals ; China ; Genitalia ; *Lepidoptera ; Mitochondria ; *Moths ; Phylogeny ; },
abstract = {Neochloroglyphica gen. nov. and its type species N. perbella sp. nov. are described from Yunnan, China. Morphological characters and molecular phylogenetic analysis, based on one mitochondrial and three nuclear genes, support the hypothesis that Neochloroglyphica is a member of the tribe Neohipparchini, and that it is a sister genus to Chloroglyphica. Morphological characters, including those of the genitalia, are figured and compared with related genera, especially Chloroglyphica, Neohipparchus and Chlororithra. Diagnoses for the genus and the species are provided and illustrations of external features and genitalia are presented.},
}

Animals
China
Genitalia
*Lepidoptera
Mitochondria
*Moths
Phylogeny

@article {pmid31711195,
year = {2019},
author = {Dourmap, C and Roque, S and Morin, A and Caubrière, D and Kerdiles, M and Béguin, K and Perdoux, R and Reynoud, N and Bourdet, L and Audebert, PA and Moullec, JL and Couée, I},
title = {Stress signalling dynamics of the mitochondrial electron transport chain and oxidative phosphorylation system in higher plants.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcz184},
pmid = {31711195},
issn = {1095-8290},
abstract = {BACKGROUND: Mitochondria play a diversity of physiological and metabolic roles under conditions of abiotic or biotic stress. They may be directly subjected to physico-chemical constraints, and they are also involved in integrative responses to environmental stresses through their central position in cell nutrition, respiration, energy balance and biosyntheses. In plant cells, mitochondria present various biochemical peculiarities, such as cyanide-insensitive alternative respiration, and, besides integration with ubiquitous eukaryotic compartments, their functioning must be coupled with plastid functioning. Moreover, given the sessile lifestyle of plants, their relative lack of protective barriers and present threats of climate change, the plant cell is an attractive model to understand the mechanisms of stress/organelle/cell integration in the context of environmental stress responses.

SCOPE: The involvement of mitochondria in this integration entails a complex network of signalling, which has not been fully elucidated, because of the great diversity of mitochondrial constituents (metabolites, reactive molecular species, structural and regulatory biomolecules) that are linked to stress signalling pathways. The present review analyses the complexity of stress signalling connexions that are related to the mitochondrial electron transport chain and oxidative phosphorylation system, and how they can be involved in stress perception and transduction, signal amplification, or cell stress response modulation.

CONCLUSIONS: Plant mitochondria are endowed with a diversity of multi-directional hubs of stress signalling that lead to regulatory loops and regulatory rheostats, whose functioning can amplify and diversify some signals or, conversely, dampen and reduce other signals. Involvement in a wide range of abiotic and biotic responses also implies that mitochondrial stress signalling could result in synergistic or conflicting outcomes during acclimation to multiple and complex stresses, such as those arising from climate change.},
}

@article {pmid31705651,
year = {2019},
author = {Igloi, GL},
title = {Molecular evidence for the evolution of the eukaryotic mitochondrial arginyl-tRNA synthetase from the prokaryotic suborder Cystobacterineae.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.13665},
pmid = {31705651},
issn = {1873-3468},
abstract = {The evolutionary origin of the family of eukaryotic aminoacyl-tRNA synthetases that are essential to all living organisms is a matter of debate. In order to shed molecular light on the ancient source of arginyl-tRNA synthetase, a total of 1347 eukaryotic arginyl-tRNA synthetase sequences were mined from databases and analyzed. Their multiple sequence alignment reveals a signature sequence that is characteristic of the nuclear-encoded enzyme, which is imported into mitochondria. Using this molecular beacon, the origins of this gene can be traced to modern prokaryotes. In this way, a previous phylogenetic analysis linking Myxococcus to the emergence of the eukaryotic mitochondrial arginyl-tRNA synthetase is supported by the unique existence of the molecular signature within the suborder Cystobacterineae that includes Myxococcus.},
}

@article {pmid31702777,
year = {2019},
author = {Wang, BJ and Xia, JM and Wang, Q and Yu, JL and Song, Z and Zhao, H},
title = {Diet and adaptive evolution of alanine-glyoxylate aminotransferase mitochondrial targeting in birds.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz266},
pmid = {31702777},
issn = {1537-1719},
abstract = {Adaptations to different diets represent a hallmark of animal diversity. The diets of birds are highly variable, making them an excellent model system for studying adaptive evolution driven by dietary changes. To test whether molecular adaptations to diet have occurred during the evolution of birds, we examined a dietary enzyme alanine-glyoxylate aminotransferase (AGT), which tends to target mitochondria in carnivorous mammals, peroxisomes in herbivorous mammals, and both mitochondria and peroxisomes in omnivorous mammals. A total of 31 bird species were examined in this study, which included representatives of most major avian lineages. Of these, 29 have an intact mitochondrial targeting sequence (MTS) of AGT. This finding is in stark contrast to mammals, which showed a number of independent losses of the MTS. Our cell-based functional assays revealed that the efficiency of AGT mitochondrial targeting was greatly reduced in unrelated lineages of granivorous birds, yet it tended to be high in insectivorous and carnivorous lineages. Furthermore, we found that proportions of animal tissue in avian diets were positively correlated with mitochondrial targeting efficiencies that were experimentally determined, but not with those that were computationally predicted. Adaptive evolution of AGT mitochondrial targeting in birds was further supported by the detection of positive selection on MTS regions. Our study contributes to the understanding of how diet drives molecular adaptations in animals, and suggests that caution must be taken when computationally predicting protein subcellular targeting.},
}

@article {pmid31697708,
year = {2019},
author = {Bénit, P and Kahn, A and Chretien, D and Bortoli, S and Huc, L and Schiff, M and Gimenez-Roqueplo, AP and Favier, J and Gressens, P and Rak, M and Rustin, P},
title = {Evolutionarily conserved susceptibility of the mitochondrial respiratory chain to SDHI pesticides and its consequence on the impact of SDHIs on human cultured cells.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224132},
pmid = {31697708},
issn = {1932-6203},
abstract = {Succinate dehydrogenase (SDH) inhibitors (SDHIs) are used worldwide to limit the proliferation of molds on plants and plant products. However, as SDH, also known as respiratory chain (RC) complex II, is a universal component of mitochondria from living organisms, highly conserved through evolution, the specificity of these inhibitors toward fungi warrants investigation. We first establish that the human, honeybee, earthworm and fungal SDHs are all sensitive to the eight SDHIs tested, albeit with varying IC50 values, generally in the micromolar range. In addition to SDH, we observed that five of the SDHIs, mostly from the latest generation, inhibit the activity of RC complex III. Finally, we show that the provision of glucose ad libitum in the cell culture medium, while simultaneously providing sufficient ATP and reducing power for antioxidant enzymes through glycolysis, allows the growth of RC-deficient cells, fully masking the deleterious effect of SDHIs. As a result, when glutamine is the major carbon source, the presence of SDHIs leads to time-dependent cell death. This process is significantly accelerated in fibroblasts derived from patients with neurological or neurodegenerative diseases due to RC impairment (encephalopathy originating from a partial SDH defect) and/or hypersensitivity to oxidative insults (Friedreich ataxia, familial Alzheimer's disease).},
}

@article {pmid31696767,
year = {2019},
author = {Ayyub, SA and Varshney, U},
title = {Translation initiation in mammalian mitochondria- a prokaryotic perspective.},
journal = {RNA biology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/15476286.2019.1690099},
pmid = {31696767},
issn = {1555-8584},
abstract = {ATP is generated in mitochondria of eukaryotic cells by oxidative phosphorylation (OXPHOS). The OXPHOS complex, which is crucial for cellular metabolism, comprises of both nuclear and mitochondrially encoded subunits. Also, the occurrence of several pathologies because of mutations in the mitochondrial translation apparatus indicates the importance of mitochondrial translation and its regulation. The mitochondrial translation apparatus is similar to its prokaryotic counterpart due to a common origin of evolution. However, mitochondrial translation has diverged from prokaryotic translation in many ways by reductive evolution. In this review, we focus on mammalian mitochondrial translation initiation, a highly regulated step of translation, and present a comparison with prokaryotic translation.},
}

@article {pmid31681764,
year = {2019},
author = {Naumann, B and Burkhardt, P},
title = {Spatial Cell Disparity in the Colonial Choanoflagellate Salpingoeca rosetta.},
journal = {Frontiers in cell and developmental biology},
volume = {7},
number = {},
pages = {231},
pmid = {31681764},
issn = {2296-634X},
abstract = {Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to the co-existence of specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial, and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to sponge choanocytes. Our analysis shows that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria, and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is slightly higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.},
}

@article {pmid31670447,
year = {2019},
author = {Surana, S and Villarroel-Campos, D and Lazo, OM and Moretto, E and Tosolini, AP and Rhymes, ER and Richter, S and Sleigh, JN and Schiavo, G},
title = {The evolution of the axonal transport toolkit.},
journal = {Traffic (Copenhagen, Denmark)},
volume = {},
number = {},
pages = {},
doi = {10.1111/tra.12710},
pmid = {31670447},
issn = {1600-0854},
abstract = {Neurons are highly polarised cells that critically depend on long-range, bidirectional transport between the cell body and synapse for their function. This continual and highly coordinated trafficking process, which takes place via the axon, has fascinated researchers since the early twentieth century. Ramon y Cajal first proposed the existence of axonal trafficking of biological material after observing that dissociation of the axon from the cell body led to neuronal degeneration. Since these first indirect observations, the field has come a long way in its understanding of this fundamental process. However, these advances in our knowledge have been aided by breakthroughs in other scientific disciplines, as well as the parallel development of novel tools, techniques and model systems. In this review, we summarise the evolution of tools used to study axonal transport and discuss how their deployment has refined our understanding of this process. We also highlight innovative tools currently being developed and how their addition to the available axonal transport toolkit might help to address key outstanding questions. This article is protected by copyright. All rights reserved.},
}

@article {pmid31669617,
year = {2019},
author = {Barros, MH and McStay, GP},
title = {Modular biogenesis of mitochondrial respiratory complexes.},
journal = {Mitochondrion},
volume = {50},
number = {},
pages = {94-114},
doi = {10.1016/j.mito.2019.10.008},
pmid = {31669617},
issn = {1872-8278},
abstract = {Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.},
}

@article {pmid31647561,
year = {2019},
author = {Lewis, WH and Lind, AE and Sendra, KM and Onsbring, H and Williams, TA and Esteban, GF and Hirt, RP and Ettema, TJG and Embley, TM},
title = {Convergent evolution of hydrogenosomes from mitochondria by gene transfer and loss.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz239},
pmid = {31647561},
issn = {1537-1719},
abstract = {Hydrogenosomes are H2-producing mitochondrial homologues found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition we generated genomic and transcriptomic datasets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.},
}

@article {pmid31640544,
year = {2019},
author = {Wang, G and Lin, J and Shi, Y and Chang, X and Wang, Y and Guo, L and Wang, W and Dou, M and Deng, Y and Ming, R and Zhang, J},
title = {Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {765},
pmid = {31640544},
issn = {1471-2164},
support = {KNJ-153011-1//Agricultural technology extension service system for edible fungus industry in Fujian, China/ ; 2016NZ0001//the Science and Technology Major Project of Fujian Province/ ; 31670021//Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells.

RESULTS: In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene.

CONCLUSIONS: Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.},
}

@article {pmid31632444,
year = {2019},
author = {Shen, X and Pu, Z and Chen, X and Murphy, RW and Shen, Y},
title = {Convergent Evolution of Mitochondrial Genes in Deep-Sea Fishes.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {925},
pmid = {31632444},
issn = {1664-8021},
abstract = {Deep seas have extremely harsh conditions including high hydrostatic pressure, total darkness, cold, and little food and oxygen. The adaptations of fishes to deep-sea environment apparently have occurred independently many times. The genetic basis of adaptation for obtaining their energy remains unknown. Mitochondria play a central role in aerobic respiration. Analyses of the available 2,161 complete mitochondrial genomes of 1,042 fishes, including 115 deep-sea species, detect signals of positive selection in mitochondrial genes in nine branches of deep-sea fishes. Aerobic metabolism yields much more energy per unit of source material than anaerobic metabolism. The adaptive evolution of the mtDNA may reflect that aerobic metabolism plays a more important role than anaerobic metabolism in deep-sea fishes, whose energy sources (food) are extremely limited. This strategy maximizes the usage of energy sources. Eleven mitochondrial genes have convergent/parallel amino acid changes between branches of deep-sea fishes. Thus, these amino acid sites may be functionally important in the acquisition of energy, and reflect convergent evolution during their independent invasion of the harsh deep-sea ecological niche.},
}

@article {pmid31631459,
year = {2019},
author = {Jelassi, R and Khemaissia, H and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K},
title = {The induced damage in the hepatopancreas of Orchestia species after exposure to a mixture of Cu/Zn-An ultrastructural study.},
journal = {Microscopy research and technique},
volume = {},
number = {},
pages = {},
doi = {10.1002/jemt.23397},
pmid = {31631459},
issn = {1097-0029},
support = {//Research Laboratory of Diversity, Management and Conservation of Biological Systems, Faculty of Science of Tunis, University of Tunis El Manar/ ; //Erasmus Mundus Al Idrisi II Programme of the European Union/ ; },
abstract = {The hepatopancreas of crustaceans species has been recognized as an essential target organ to assess trace elements' effects. Due to its dynamic and capability of detoxifying trace metal, this organ often indicates distinct pathological disturbances. In the present work, we intend to evaluate the bioaccumulation of trace metal in three Orchestia species (Orchestia montagui, Orchestia gammarellus, and Orchestia mediterranea) living in symmetry in the banks of Bizerte lagoon (37°13'8″N 09°55'1″E) after their exposure during 14 days to a mixture of copper and zinc, and to highlight the effect of these metals on their hepatopancreas ultrastructure using transmission electron microscopy. At the end of the experiment, results showed that the mortality and the body mass varied according to the used nominal concentrations. Significant alterations were noted in all the treatment groups. The degree of these alterations depends on the used concentration, and they are represented especially by the cells remoteness and the border lyses, the reduction of the nuclear volume, the increase in the cytoplasm density with the presence of trace metal in the nucleus as well as in the vacuole, the disorganization and the destruction of microvilli, the condensation of the majority of cellular organelles and mitochondria swelling. Through this study, Orchestia genus could be an attractive candidate for the biochemical study of trace metal toxicity in Tunisian wetlands.},
}

@article {pmid31630458,
year = {2019},
author = {Small, ID and Schallenberg-Rüdinger, M and Takenaka, M and Mireau, H and Ostersetzer-Biran, O},
title = {Plant organellar RNA editing: what 30 years of research has revealed.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.14578},
pmid = {31630458},
issn = {1365-313X},
abstract = {The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-to-U base transitions) is highly prevalent within organelles (i.e., mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.},
}

@article {pmid31630139,
year = {2019},
author = {Ozozan, OV and Dinc, T and Vural, V and Ozogul, C and Ozmen, MM and Coskun, F},
title = {An electron microscopy study of liver and kidney damage in an experimental model of obstructive jaundice.},
journal = {Annali italiani di chirurgia},
volume = {8},
number = {},
pages = {},
pmid = {31630139},
issn = {2239-253X},
abstract = {With this experimental study we investigated the consequences of ligation of the common bile duct (CBD) on hepatic cells and on the renal ultrastructure by electron microscopy and also determine the effects after liberation of the ductus joint in order to clarify the mechanisms of renal failure commonly observed in cholestatic liver disease. The study was conducted on 53 Wistar albino rats divided into 4 subgroups. In the comparison group (sham) we proceeded to the simple laparotomy. After preparation of the common bile duct of all the rats of the four groups, and ligation of the duct at the level of the distal third, eight rats in each group were sacrificed on the 3rd, 7th, 10th and 14th day after surgery, taking blood samples to measure the serum levels of ALP and bilirubin, and liver and renal tissue samples for histological evaluation. In four rats of each group the common bile duct was unligated at the same deadlines to obtain free drainage of the bile for a week. At the end of this week, the rats were sacrificed by collecting blood and liver and kidney tissue samples.

RESULTS: after CBD ligation in both groups, the ALP value, total and direct bilurubin levels were proportionally increased. After duct release, bilurubin levels decreased significantly. In group II, while large lipid granules were observed to indicate oxidative damage, mitochondrial swelling and crystals were observed after duct liberation. Areas of glycogen and normal mitochondria were observed in group IV. After duct release in this group, increases in Ito granules, lipid granules and normal mitochondria were observed, which may reflect the evolution of hepatic regeneration. When renal tissue was examined in group II, fusion processes in the feet, thickening of the basement membrane and mesengium were observed, and mitochondrial crystals were observed in renal tissue as well as in the liver after duct release. Damage in group III and group IV was increased parallel to prolongation of jaundice and after loosening persistent damage with mitochondrial crystals.

CONCLUSION: Ultrastructural changes in rat liver tissue in conditions of obstructive jaundice may be reversible after restoration of drainage. On the other hand, ultrastructural changes in renal tissue in cases of prolonged jaundice are irreversible even if the internal drainage is restored.

KEY WORDS: Bile Duct, Liver, Kidney, Obstructive Jaundice.},
}

@article {pmid31617565,
year = {2019},
author = {Žihala, D and Eliáš, M},
title = {Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae.},
journal = {Genome biology and evolution},
volume = {11},
number = {10},
pages = {2992-3007},
pmid = {31617565},
issn = {1759-6653},
abstract = {Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.},
}

@article {pmid31611421,
year = {2019},
author = {Khoshravesh, R and Stata, M and Busch, FA and Saladie, M and Castelli, JM and Dakin, N and Hattersley, PW and Macfarlane, TD and Sage, RF and Ludwig, M and Sage, TL},
title = {The Evolutionary Origin of C4 photosynthesis in the Grass Subtribe Neurachninae.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1104/pp.19.00925},
pmid = {31611421},
issn = {1532-2548},
abstract = {The Australian grass subtribe Neurachninae contains closely related species that use C3, C4 and C2 photosynthesis. To gain insight into the evolution of C4 photosynthesis in grasses, we examined leaf gas exchange, anatomy and ultrastructure, and tissue localization of glycine decarboxylase subunit P (GLDP) in nine Neurachninae species. We identified previously unrecognized variation in leaf structure and physiology within Neurachne that represents varying degrees of C3-C4 intermediacy in the Neurachninae. These include inverse correlations between the apparent photosynthetic CO2 compensation point in the absence of day respiration (C*) and a) chloroplast and mitochondrial investment in the mestome sheath (MS), where CO2 is concentrated in C2 and C4 Neurachne species; b) width of the MS cells; c) frequency of plasmodesmata in the MS cell walls adjoining the parenchymatous bundle sheath; and d) the proportion of leaf GLDP invested in the MS tissue. Less than 12% of the leaf GLDP was allocated to the MS of completely C3 Neurachninae species with C* values of 56-61 µmol mol-1, whereas two-thirds of leaf GLDP was in the MS of Neurachne lanigera, which exhibits a newly-identified, partial C2 phenotype with C* of 44 µmol mol-1. Increased investment of GLDP in MS tissue of the C2 species was attributed to more MS mitochondria and less GLDP in mesophyll mitochondria. These results are consistent with a model where C4 evolution in Neurachninae initially occurred via an increase in organelle and GLDP content in MS cells, which generated a sink for photorespired CO2 in MS tissues.},
}

@article {pmid31599941,
year = {2019},
author = {Liu, Q and Lin, D and Li, M and Gu, Z and Zhao, Y},
title = {Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma.},
journal = {Genome biology and evolution},
volume = {11},
number = {10},
pages = {2909-2916},
pmid = {31599941},
issn = {1759-6653},
abstract = {Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from 1 nontumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only 2 heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers, and single-nucleotide variants in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent nontumor tissue, and they both likely evolved under neutral selection.},
}

@article {pmid31591397,
year = {2019},
author = {Smith, SR and Dupont, CL and McCarthy, JK and Broddrick, JT and Oborník, M and Horák, A and Füssy, Z and Cihlář, J and Kleessen, S and Zheng, H and McCrow, JP and Hixson, KK and Araújo, WL and Nunes-Nesi, A and Fernie, A and Nikoloski, Z and Palsson, BO and Allen, AE},
title = {Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4552},
pmid = {31591397},
issn = {2041-1723},
abstract = {Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.},
}