@article {pmid30208839,
year = {2018},
author = {Bono, JM and Pigage, HK and Wettstein, PJ and Prosser, SA and Pigage, JC},
title = {Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {139},
pmid = {30208839},
issn = {1471-2148},
mesh = {Animals ; *Biological Evolution ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetic Variation ; *Genome ; Geography ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sciuridae/*genetics ; },
abstract = {BACKGROUND: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested.

RESULTS: We used RAD-seq to unravel the complex evolutionary history of the Abert's squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon.

CONCLUSIONS: Overall, the evolutionary history of Abert's squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.},
}

Animals
*Biological Evolution
Cytochromes b/genetics
DNA, Mitochondrial/genetics
Genetic Markers
*Genetic Variation
*Genome
Geography
Haplotypes/genetics
Likelihood Functions
Mitochondria/genetics
Phylogeography
Polymorphism, Single Nucleotide/genetics
Principal Component Analysis
Sciuridae/*genetics

@article {pmid29950599,
year = {2018},
author = {Burgstaller, JP and Kolbe, T and Havlicek, V and Hembach, S and Poulton, J and Piálek, J and Steinborn, R and Rülicke, T and Brem, G and Jones, NS and Johnston, IG},
title = {Large-scale genetic analysis reveals mammalian mtDNA heteroplasmy dynamics and variance increase through lifetimes and generations.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2488},
doi = {10.1038/s41467-018-04797-2},
pmid = {29950599},
issn = {2041-1723},
support = {MR/J013617/1//Medical Research Council/United Kingdom ; },
mesh = {Age Factors ; Animals ; DNA Copy Number Variations/*genetics ; DNA, Mitochondrial/*genetics ; Datasets as Topic ; Female ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Mice ; Mice, Inbred C57BL ; Mitochondria/metabolism ; Models, Animal ; Oocytes/cytology/immunology ; },
abstract = {Vital mitochondrial DNA (mtDNA) populations exist in cells and may consist of heteroplasmic mixtures of mtDNA types. The evolution of these heteroplasmic populations through development, ageing, and generations is central to genetic diseases, but is poorly understood in mammals. Here we dissect these population dynamics using a dataset of unprecedented size and temporal span, comprising 1947 single-cell oocyte and 899 somatic measurements of heteroplasmy change throughout lifetimes and generations in two genetically distinct mouse models. We provide a novel and detailed quantitative characterisation of the linear increase in heteroplasmy variance throughout mammalian life courses in oocytes and pups. We find that differences in mean heteroplasmy are induced between generations, and the heteroplasmy of germline and somatic precursors diverge early in development, with a haplotype-specific direction of segregation. We develop stochastic theory predicting the implications of these dynamics for ageing and disease manifestation and discuss its application to human mtDNA dynamics.},
}

Age Factors
Animals
DNA Copy Number Variations/*genetics
DNA, Mitochondrial/*genetics
Datasets as Topic
Female
Genome, Mitochondrial/*genetics
Haplotypes/genetics
Mice
Mice, Inbred C57BL
Mitochondria/metabolism
Models, Animal
Oocytes/cytology/immunology

@article {pmid29385875,
year = {2018},
author = {Mustafa, SI and Schwarzacher, T and Heslop-Harrison, JS},
title = {Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {8},
pages = {1180-1193},
doi = {10.1080/24701394.2018.1431226},
pmid = {29385875},
issn = {2470-1408},
mesh = {Animals ; Breeding ; Centromere/*genetics ; *Evolution, Molecular ; Female ; *Genetic Speciation ; *Genome, Mitochondrial ; Male ; Polymorphism, Single Nucleotide ; Sex Chromosomes/genetics ; Sheep/*genetics ; },
abstract = {The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the 'Fertile Crescent'. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.},
}

Animals
Breeding
Centromere/*genetics
*Evolution, Molecular
Female
*Genetic Speciation
*Genome, Mitochondrial
Male
Polymorphism, Single Nucleotide
Sex Chromosomes/genetics
Sheep/*genetics

@article {pmid28667281,
year = {2017},
author = {Yang, F and Jiang, Y and Yang, D and Liu, X},
title = {Mitochondrial genomes of two Australian fishflies with an evolutionary timescale of Chauliodinae.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4481},
pmid = {28667281},
issn = {2045-2322},
mesh = {Animals ; Australia ; Base Composition ; Codon ; Computational Biology/methods ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genomics/methods ; Insecta/*classification/*genetics ; Mitochondria/genetics ; Nucleic Acid Conformation ; Phylogeny ; },
abstract = {Fishflies (Corydalidae: Chauliodinae) with a total of ca. 130 extant species are one of the major groups of the holometabolous insect order Megaloptera. As a group which originated during the Mesozoic, the phylogeny and historical biogeography of fishflies are of high interest. The previous hypothesis on the evolutionary history of fishflies was based primarily on morphological data. To further test the existing phylogenetic relationships and to understand the divergence pattern of fishflies, we conducted a molecule-based study. We determined the complete mitochondrial (mt) genomes of two Australian fishfly species, Archichauliodes deceptor Kimmins, 1954 and Protochauliodes biconicus Kimmins, 1954, both members of a major subgroup of Chauliodinae with high phylogenetic significance. A phylogenomic analysis was carried out based on 13 mt protein coding genes (PCGs) and two rRNAs genes from the megalopteran species with determined mt genomes. Both maximum likelihood and Bayesian inference analyses recovered the Dysmicohermes clade as the sister group of the Archichauliodes clade + the Protochauliodes clade, which is consistent with the previous morphology-based hypothesis. The divergence time estimation suggested that the divergence among the three major subgroups of fishflies occurred during the Late Jurassic and Early Cretaceous when the supercontinent Pangaea was undergoing sequential breakup.},
}

Animals
Australia
Base Composition
Codon
Computational Biology/methods
*Evolution, Molecular
Genes, Mitochondrial
*Genome, Mitochondrial
Genomics/methods
Insecta/*classification/*genetics
Mitochondria/genetics
Nucleic Acid Conformation
Phylogeny

@article {pmid30621777,
year = {2018},
author = {Lynch, M and Marinov, GK},
title = {Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells.},
journal = {Biology direct},
volume = {13},
number = {1},
pages = {26},
doi = {10.1186/s13062-018-0228-3},
pmid = {30621777},
issn = {1745-6150},
abstract = {A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mitochondrion endowed eukaryotic cells with energetic superiority over prokaryotes. The former point has been addressed previously, with no resultant changes in the conclusions, and the latter point remains inconsistent with multiple lines of empirical data.},
}

@article {pmid28655921,
year = {2017},
author = {Liu, H and Li, H and Song, F and Gu, W and Feng, J and Cai, W and Shao, R},
title = {Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4284},
pmid = {28655921},
issn = {2045-2322},
mesh = {Animals ; Evolution, Molecular ; *Gene Rearrangement ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Thysanoptera/classification/*genetics ; },
abstract = {We sequenced the mitochondrial (mt) genome of the grass thrips, Anaphothrips obscurus, which is highly rearranged and differs from the four thrips species reported previously in the arrangement of both tRNA genes and a protein-coding gene, nad3, and in the copy number of the control region (CR). We reconstructed the phylogeny of the thrips with mt genome sequences, and used it as a framework to gain insights into mt genome evolution in thrips. It is evident that A. obscurus is less rearranged in mt genome organization than the other four known thrips. nad3 is in its ancestral location in A. obscurus but was translocated in other four thrips. Also, A. obscurus has one CR, which is ancestral to hexapods whereas other thrips have two or three CRs. All of the five thrips whose mt genomes have been sequenced to date are from the subfamily Thripinae, which represents about a quarter of the species richness in the order Thysanoptera. The high variation in mt genome organization observed in a subfamily challenges our knowledge about animal mt genomes. It remains to be investigated why mt genomes evolved so fast in the subfamily Thripinae and how mt genomes evolved in other lineages of thrips.},
}

Animals
Evolution, Molecular
*Gene Rearrangement
Genes, Mitochondrial
Genome, Mitochondrial
Genomics/methods
High-Throughput Nucleotide Sequencing
Mitochondria/*genetics
Phylogeny
Thysanoptera/classification/*genetics

@article {pmid28655915,
year = {2017},
author = {Bernardino, AF and Li, Y and Smith, CR and Halanych, KM},
title = {Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4295},
pmid = {28655915},
issn = {2045-2322},
mesh = {Animals ; Annelida/classification/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Introns ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Wood falls provide episodic fluxes of energy to the sea floor that are degraded by a species-rich benthic fauna. Part of this rich diversity includes annelid polychaetes but unfortunately, our understanding of such fauna is limited and their genetic variability and evolutionary origins remain poorly known. In this study, we sequenced complete mitochondrial genomes from three congeneric Decemunciger (Ampharetidae) individuals that had colonized multiple wood falls in the deep (~1600 m) NE Pacific Ocean. Mitochondrial gene order within Decemunciger was similar to the three other available Terebellomorpha genomes, consistent with the relatively conserved nature of mitochondrial genomes within annelids. Unexpectedly, we found introns within the cox1, nad1 and nad4 genes of all three genomes assembled. This is the greatest number of introns observed in annelid mtDNA genomes, and possibly in bilaterians. Interestingly, the introns were of variable sizes suggesting possible evolutionary differences in the age and origins of introns. The sequence of the introns within cox1 is similar to Group II introns previously identified, suggesting that introns in the mitochondrial genome of annelids may be more widespread then realized. Phylogenetically, Decemunciger appears to be a sister clade among current vent and seep deep-sea Ampharetinae.},
}

Animals
Annelida/classification/*genetics
Genes, Mitochondrial
*Genome, Mitochondrial
*Introns
Mitochondria/*genetics
Phylogeny
Sequence Analysis, DNA

@article {pmid30612859,
year = {2018},
author = {Adlakha, J and Karamichali, I and Sangwallek, J and Deiss, S and Bär, K and Coles, M and Hartmann, MD and Lupas, AN and Hernandez Alvarez, B},
title = {Characterization of MCU-Binding Proteins MCUR1 and CCDC90B - Representatives of a Protein Family Conserved in Prokaryotes and Eukaryotic Organelles.},
journal = {Structure (London, England : 1993)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.str.2018.11.004},
pmid = {30612859},
issn = {1878-4186},
abstract = {Membrane-bound coiled-coil proteins are important mediators of signaling, fusion, and scaffolding. Here, we delineate a heterogeneous group of trimeric membrane-anchored proteins in prokaryotes and eukaryotic organelles with a characteristic head-neck-stalk-anchor architecture, in which a membrane-anchored coiled-coil stalk projects an N-terminal head domain via a β-layer neck. Based on sequence analysis, we identify different types of head domains and determine crystal structures of two representatives, the archaeal protein Kcr-0859 and the human CCDC90B, which possesses the most widespread head type. Using mitochondrial calcium uniporter regulator 1 (MCUR1), the functionally characterized paralog of CCDC90B, we study the role of individual domains, and find that the head interacts directly with the mitochondrial calcium uniporter (MCU) and is destabilized upon Ca2+ binding. Our data provide structural details of a class of membrane-bound coiled-coil proteins and identify the conserved head domain of the most widespread type as a mediator of their function.},
}

@article {pmid30204084,
year = {2018},
author = {Seidi, A and Muellner-Wong, LS and Rajendran, E and Tjhin, ET and Dagley, LF and Aw, VY and Faou, P and Webb, AI and Tonkin, CJ and van Dooren, GG},
title = {Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
pmid = {30204084},
issn = {2050-084X},
support = {DP110103144//Australian Research Council/International ; },
mesh = {Animals ; Biotinylation ; Computational Biology ; Electron Transport Complex IV/*metabolism ; Gene Knockdown Techniques ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; Oxygen Consumption ; Parasites/growth & development/metabolism ; Phenotype ; Phylogeny ; Proteome/*metabolism ; Proteomics ; Protozoan Proteins/metabolism ; Toxoplasma/growth & development/*metabolism ; },
abstract = {The mitochondrion of apicomplexan parasites is critical for parasite survival, although the full complement of proteins that localize to this organelle has not been defined. Here we undertake two independent approaches to elucidate the mitochondrial proteome of the apicomplexan Toxoplasma gondii. We identify approximately 400 mitochondrial proteins, many of which lack homologs in the animals that these parasites infect, and most of which are important for parasite growth. We demonstrate that one such protein, termed TgApiCox25, is an important component of the parasite cytochrome c oxidase (COX) complex. We identify numerous other apicomplexan-specific components of COX, and conclude that apicomplexan COX, and apicomplexan mitochondria more generally, differ substantially in their protein composition from the hosts they infect. Our study highlights the diversity that exists in mitochondrial proteomes across the eukaryotic domain of life, and provides a foundation for defining unique aspects of mitochondrial biology in an important phylum of parasites.},
}

Animals
Biotinylation
Computational Biology
Electron Transport Complex IV/*metabolism
Gene Knockdown Techniques
Mitochondria/*metabolism
Mitochondrial Membranes/metabolism
Mitochondrial Proteins/metabolism
Oxygen Consumption
Parasites/growth & development/metabolism
Phenotype
Phylogeny
Proteome/*metabolism
Proteomics
Protozoan Proteins/metabolism
Toxoplasma/growth & development/*metabolism

@article {pmid29656105,
year = {2018},
author = {Dias, C and Lima, KA and Araripe, J and Aleixo, A and Vallinoto, M and Sampaio, I and Schneider, H and Rêgo, PSD},
title = {Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae).},
journal = {Molecular phylogenetics and evolution},
volume = {126},
number = {},
pages = {314-320},
doi = {10.1016/j.ympev.2018.04.017},
pmid = {29656105},
issn = {1095-9513},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Passeriformes/*classification/*genetics ; *Phylogeny ; },
abstract = {Lepidothrix is the most diverse genus of the family Pipridae, with eight recognized species. Although the genus' monophyly has been supported by both molecular and morphological characters, phylogenetic relationships and species limits within Lepidothrix remain uncertain. In the present study, we combined molecular sequences of mitochondrial (ND2 and COI) and nuclear (MYO, G3PDh and I5BF) markers in a multilocus analysis, to evaluate relationships and inter-specific limits among L. iris, L. nattereri, and L. vilasboasi, which are known to hybridize in eastern Amazonia. The results revealed a complex pattern, whereby events of secondary contact and gene flow after isolation and genetic and phenotypic differentiation prevented the recuperation of reciprocal monophyly among the studied taxa. The mitochondrial data indicate that L. nattereri is divided into two non-sister groups, one monophyletic, and the other, paraphyletic, with L. iris iris being more closely related to one of the two L. nattereri groups, while L. iris eucephala forms an undifferentiated clade with L. vilasboasi, probably resulting from an extensive process of mitochondrial introgression. In agreement with a previous study based on Single Nucleotide Polymorphism (SNP) data, mitochondrial haplotype networks also support that L. vilasboasi does not represent a recent "hybrid swarm" between L. iris and L. nattereri, but instead a genetically divergent lineage with a separate species status. Finally, the sister relationship recovered herein between L. iris iris and some western populations of L. nattereri currently in allopatry is also apparently explained by mitochondrial introgression, as also supported for nuclear genes by SNP data, indicating a complex scenario of past contact and gene flow between currently geographically distant Lepidothrix lineages.},
}

Animals
DNA, Mitochondrial/genetics
Haplotypes/genetics
Mitochondria/*genetics
Passeriformes/*classification/*genetics
*Phylogeny

@article {pmid29524652,
year = {2018},
author = {Berriman, JS and Ellingson, RA and Awbrey, JD and Rico, DM and Valdés, ÁA and Wilson, NG and Aguilar, A and Herbert, DG and Hirano, YM and Trowbridge, CD and Krug, PJ},
title = {A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume "killer algae".},
journal = {Molecular phylogenetics and evolution},
volume = {126},
number = {},
pages = {356-370},
pmid = {29524652},
issn = {1095-9513},
support = {R25 GM061331/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; Biodiversity ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Eukaryota/*physiology ; Gastropoda/*physiology ; Genetic Variation ; Haplotypes/genetics ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; Tooth/*physiology ; },
abstract = {Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.},
}

Animals
Bayes Theorem
Biodiversity
DNA, Mitochondrial/genetics
Electron Transport Complex IV/genetics
Eukaryota/*physiology
Gastropoda/*physiology
Genetic Variation
Haplotypes/genetics
Mitochondria/genetics
*Phylogeny
Species Specificity
Tooth/*physiology

@article {pmid28607415,
year = {2017},
author = {Hofmann, S and Stöck, M and Zheng, Y and Ficetola, FG and Li, JT and Scheidt, U and Schmidt, J},
title = {Molecular Phylogenies indicate a Paleo-Tibetan Origin of Himalayan Lazy Toads (Scutiger).},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {3308},
pmid = {28607415},
issn = {2045-2322},
mesh = {Animals ; Anura/*classification ; Calibration ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Geography ; Mitochondria/genetics ; *Phylogeny ; Tibet ; Time Factors ; },
abstract = {The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the "Tibetan-origin hypothesis" suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a "Tibetan-origin hypothesis", current sampling (10/22 species; 1 revalidated: S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.},
}

Animals
Anura/*classification
Calibration
Cell Nucleus/genetics
DNA, Mitochondrial/genetics
Electron Transport Complex IV/genetics
Genetic Markers
Geography
Mitochondria/genetics
*Phylogeny
Tibet
Time Factors

@article {pmid30612363,
year = {2019},
author = {Jelassi, R and Khemaissia, H and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K},
title = {Ecotoxicological effects of trace element contamination in talitrid amphipod Orchestia montagui Audouin, 1826.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-018-3974-y},
pmid = {30612363},
issn = {1614-7499},
abstract = {This study deals with the evaluation of trace element bioaccumulation and histological alterations in the hepatopancreas of the supralittoral amphipod Orchestia montagui Audouin, 1826 due to the exposure to cadmium, copper, and zinc. Orchestia montagui individuals were maintained during 14 days in soils contaminated with different trace elements namely cadmium, copper, and zinc; a control was also prepared. Our results show that the mortality and the body mass vary according to the metal and the nominal concentration used. In general, the mortality increases from the seventh day. However, the body mass shows a decrease with cadmium exposure and an increase with copper and zinc exposures. Furthermore, the concentration factor highlights that this species is considered a macroconcentrator for copper and zinc. The hepatopancreas of unexposed and exposed animals were compared to detect histological changes. Our results show significant alterations in the hepatopancreas of the exposed animals after the experiment. The degree of these alterations was found to be dose-dependent. Among the histological changes in the hepatopancreas in O. montagui, a loss of cell structure was noted, especially cell remoteness and border lyses, the reduction of nuclear volume, an increase in the cytoplasm density with the presence of trace element deposits in both the nucleus and vacuoles, a disorganization and destruction of microvilli, and a condensation of the majority of cell organelles and mitochondria swelling. Through this study, we have confirmed that O. montagui can be a relevant model to assess trace metal element pollution in Tunisian coastal lagoons with the aim of using it in future biomonitoring programs.},
}

@article {pmid30280695,
year = {2018},
author = {Önder, Z and İnci, A and Yıldırım, A and Çiloğlu, A and Düzlü, Ö},
title = {Molecular Characterization of Myiasis-Causing Moth Flies (Diptera: Psychodidae).},
journal = {Turkiye parazitolojii dergisi},
volume = {42},
number = {3},
pages = {223-228},
doi = {10.5152/tpd.2018.5943},
pmid = {30280695},
issn = {2146-3077},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry ; Mitochondria/genetics ; Myiasis/*parasitology ; Phylogeny ; Psychodidae/classification/*genetics ; Sequence Alignment ; Turkey ; },
abstract = {OBJECTIVE: The aim of this study is to examine the molecular characterization of moth flies (Diptera: Psychodidae) based on their mitochondrial DNA sequences and determine the vectorial potential and damage caused by moth flies in future researches.

METHODS: A total of 240 adult moth flies were collected from toilet, bathroom, and basement walls of houses from different locations of the Kayseri region between May 2016 and April 2017. The polymerase chain reaction (PCR) analyses were performed using primer pairs, specificaly targeting the mitochondrial cytochrome oxidase c subunit I (mt-COI) gene of adult flies.

RESULTS: In total, five isolates were gel purified and sequenced for molecular characterization and phylogenetic analyses. Two species, namely Telmatoscopus albipunctatus (ERU-Telmatos3 and ERU-Telmatos6) and Psychodidae sp. (ERU-Psycho1,4,5), were successfully identified with the sequence alignment of isolates. According to the phylogenetic analysis, it was determined that the ERU-Telmatos3 and ERU-Telmatos6 isolates are clustered in the haplogroup A, while the ERU-Psycho1,4,5 isolate was clustered within the haplogroup B. The ERU-Psycho1 isolate was characterized as a new haplotype within the haplogroup B.

CONCLUSION: This study represents the first molecular characterization and phylogenetic status of moth flies in Turkey. The obtained findings should be the first step in the future investigation based on detecting the transmission of bacterial pathogens by moth flies.},
}

Animals
Base Sequence
DNA, Mitochondrial/chemistry
Mitochondria/genetics
Myiasis/*parasitology
Phylogeny
Psychodidae/classification/*genetics
Sequence Alignment
Turkey

@article {pmid30604579,
year = {2019},
author = {Huang, S and Braun, HP and Gawryluk, RMR and Millar, AH},
title = {Mitochondrial complex II of plants: subunit composition, assembly and function in respiration and signaling.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.14227},
pmid = {30604579},
issn = {1365-313X},
abstract = {Complex II (succinate dehydrogenase [succinate-ubiquinone oxidoreductase]; EC 1.3.5.1; SDH) is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. Complex II in plants is considered unusual due to its accessory subunits (SDH5-8) in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1-4). Here we review compositional and phylogenetic analysis, and biochemical dissection studies to clarify the presence and to propose the role of these subunits. We also consider the wider functional and phylogenetic evidence for SDH assembly factors and the reports from plants on the control of SDH1 flavination and SDH1-SDH2 interaction. Plant Complex II has been shown to influence stomatal opening, the plant defence response and reactive oxygen species-dependent stress responses. Signalling molecules such as salicyclic acid (SA) and nitric oxide (NO) are also reported to interact with the UQ binding site of SDH, influencing signalling transduction in plants. Future directions for SDH research in plants and the specific roles of its different subunits and assembly factors are suggested, including the potential for reverse electron transport to explain succinate-dependent ROS production in plants and new avenues to explore plant mitochondrial Complex II evolution and its utility. This article is protected by copyright. All rights reserved.},
}

@article {pmid30598556,
year = {2018},
author = {Rathore, S and Berndtsson, J and Marin-Buera, L and Conrad, J and Carroni, M and Brzezinski, P and Ott, M},
title = {Cryo-EM structure of the yeast respiratory supercomplex.},
journal = {Nature structural & molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41594-018-0169-7},
pmid = {30598556},
issn = {1545-9985},
abstract = {Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III2IV and III2IV2, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.},
}

@article {pmid30598467,
year = {2018},
author = {Clergeot, PH and Rode, NO and Glémin, S and Brandström-Durling, M and Ihrmark, K and Olson, Å},
title = {Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1534/genetics.118.301855},
pmid = {30598467},
issn = {1943-2631},
abstract = {Many eukaryote species including taxa such as fungi or algae have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance, a measure that accounts for these two effects, should be close to 0.5 in these species. They also predict that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum, a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.},
}

@article {pmid30595847,
year = {2018},
author = {Su-Keene, EJ and Bonilla, MM and Padua, MV and Zeh, DW and Zeh, JA},
title = {Simulated climate warming and mitochondrial haplogroup modulate testicular small non-coding RNA expression in the neotropical pseudoscorpion, Cordylochernes scorpioides.},
journal = {Environmental epigenetics},
volume = {4},
number = {4},
pages = {dvy027},
doi = {10.1093/eep/dvy027},
pmid = {30595847},
issn = {2058-5888},
abstract = {Recent theory suggests that tropical terrestrial arthropods are at significant risk from climate warming. Metabolic rate in such ectothermic species increases exponentially with environmental temperature, and a small temperature increase in a hot environment can therefore have a greater physiological impact than a large temperature increase in a cool environment. In two recent studies of the neotropical pseudoscorpion, Cordylochernes scorpioides, simulated climate warming significantly decreased survival, body size and level of sexual dimorphism. However, these effects were minor compared with catastrophic consequences for male fertility and female fecundity, identifying reproduction as the life stage most vulnerable to climate warming. Here, we examine the effects of chronic high-temperature exposure on epigenetic regulation in C. scorpioides in the context of naturally occurring variation in mitochondrial DNA. Epigenetic mechanisms, including DNA methylation, histone modifications and small non-coding RNA (sncRNA) expression, are particularly sensitive to environmental factors such as temperature, which can induce changes in epigenetic states and phenotypes that may be heritable across generations. Our results indicate that exposure of male pseudoscorpions to elevated temperature significantly altered the expression of >60 sncRNAs in testicular tissue, specifically microRNAs and piwi-interacting RNAs. Mitochondrial haplogroup was also a significant factor influencing both sncRNAs and mitochondrial gene expression. These findings demonstrate that chronic heat stress causes changes in epigenetic profiles that may account for reproductive dysfunction in C. scorpioides males. Moreover, through its effects on epigenetic regulation, mitochondrial DNA polymorphism may provide the potential for an adaptive evolutionary response to climate warming.},
}

@article {pmid30592713,
year = {2018},
author = {DiMaio, J and Ruthel, G and Cannon, JJ and Malfara, MF and Povelones, ML},
title = {The single mitochondrion of the kinetoplastid parasite Crithidia fasciculata is a dynamic network.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0202711},
doi = {10.1371/journal.pone.0202711},
pmid = {30592713},
issn = {1932-6203},
abstract = {Mitochondria are central organelles in cellular metabolism. Their structure is highly dynamic, allowing them to adapt to different energy requirements, to be partitioned during cell division, and to maintain functionality. Mitochondrial dynamics, including membrane fusion and fission reactions, are well studied in yeast and mammals but it is not known if these processes are conserved throughout eukaryotic evolution. Kinetoplastid parasites are some of the earliest-diverging eukaryotes to retain a mitochondrion. Each cell has only a single mitochondrial organelle, making them an interesting model for the role of dynamics in controlling mitochondrial architecture. We have investigated the mitochondrial division cycle in the kinetoplastid Crithidia fasciculata. The majority of mitochondrial biogenesis occurs during the G1 phase of the cell cycle, and the mitochondrion is divided symmetrically in a process coincident with cytokinesis. Live cell imaging revealed that the mitochondrion is highly dynamic, with frequent changes in the topology of the branched network. These remodeling reactions include tubule fission, fusion, and sliding, as well as new tubule formation. We hypothesize that the function of this dynamic remodeling is to homogenize mitochondrial contents and to facilitate rapid transport of mitochondria-encoded gene products from the area containing the mitochondrial nucleoid to other parts of the organelle.},
}

@article {pmid30592414,
year = {2018},
author = {Li, J and Liu, X and Zhang, H and Ge, X and Tang, Y and Xu, Z and Tian, L and Yuan, X and Mao, X and Liu, Z},
title = {Ferrocenyl-Triphenyltin Complexes as Lysosome-Targeted Imaging and Anticancer Agents.},
journal = {Inorganic chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.inorgchem.8b03305},
pmid = {30592414},
issn = {1520-510X},
abstract = {In this paper, two ferrocenyl-triphenyltin complexes were synthesized and characterized. Complex 2 is constructed as new multifunctional therapeutic platform for lysosome-targeted imaging and displayed much higher cytotoxicity than its analogue 1 by the introduction of a methyl group instead of a hydrogen atom in acylhydrazone. The cyclic voltammograms and reaction with GSH (glutathione) further confirmed that complex 1 has a reversible redox peak and can react with GSH, which indicate that complex 1 might lose its anticancer effect by undergoing reaction with GSH once it enters the cancer cell. Complex 2 could effectively catalyze the oxidation of NADH (the reduced form of nicotinamide adenine dinucleotide) to NAD+ and induce the production of reactive oxygen species (ROS), lead to caspase-dependent apoptosis through damaged mitochondria, simultaneously, accounting for the mitochondrial vacuolization and karyorrhexis. The caspase-3 activation and cytoplasmic vacuolation karyorrhexis induced by complex 2 revealed that the A549 cell lines might undergo cell death primarily mediated by apoptosis and oncosis; however, 1 cannot reproduce this effect. Taken together, these results indicated that complex 2 has more potential for evolution as a new bioimaging and anticancer agent.},
}

@article {pmid30590727,
year = {2018},
author = {Tsitsekian, D and Daras, G and Alatzas, A and Templalexis, D and Hatzopoulos, P and Rigas, S},
title = {Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/ery440},
pmid = {30590727},
issn = {1460-2431},
abstract = {The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.},
}

@article {pmid30588726,
year = {2018},
author = {Hill, GE and Havird, JC and Sloan, DB and Burton, RS and Greening, C and Dowling, DK},
title = {Assessing the fitness consequences of mitonuclear interactions in natural populations.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.12493},
pmid = {30588726},
issn = {1469-185X},
support = {FT160100022, DP170100165, DE170100310//Australian Research Council/ ; HSF 15/2//Hermon Slade Foundation/ ; R01 GM118046//National Institutes of Health (NIH)/ ; DEB1551466//National Science Foundation (NSF)/ ; },
abstract = {Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.},
}

@article {pmid30059499,
year = {2018},
author = {Gao, B and Peng, C and Chen, Q and Zhang, J and Shi, Q},
title = {Mitochondrial genome sequencing of a vermivorous cone snail Conus quercinus supports the correlative analysis between phylogenetic relationships and dietary types of Conus species.},
journal = {PloS one},
volume = {13},
number = {7},
pages = {e0193053},
pmid = {30059499},
issn = {1932-6203},
mesh = {Animals ; Annelida ; Base Composition ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Conotoxins/*genetics ; Conus Snail/classification/*genetics ; Food Chain ; Gene Ontology ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Tandem Repeat Sequences ; },
abstract = {Complete mitochondrial genome (mitogenome) sequence of a worm-hunting cone snail, Conus quercinus, was reported in this study. Its mitogenome, the longest one (16,460 bp) among reported Conus specie, is composed of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one D-loop region. The mitochondrial gene arrangement is highly-conserved and identical to other reported. However, the D-loop region of C. quercinus is the longest (943 bp) with the higher A+T content (71.3%) and a long AT tandem repeat stretch (68 bp). Subsequent phylogenetic analysis demonstrated that three different dietary types (vermivorous, molluscivorous and piscivorous) of cone snails are clustered separately, suggesting that the phylogenetics of cone snails is related to their dietary types. In conclusion, our current work improves our understanding of the mitogenomic structure and evolutionary status of the vermivorous C. quercinus, which support the putative hypothesis that the Conus ancestor was vermivorous.},
}

Animals
Annelida
Base Composition
Base Sequence
Biological Evolution
Chromosome Mapping
Conotoxins/*genetics
Conus Snail/classification/*genetics
Food Chain
Gene Ontology
Genome Size
*Genome, Mitochondrial
Mitochondria/*genetics
Molecular Sequence Annotation
Open Reading Frames
Phylogeny
RNA, Ribosomal/*genetics
RNA, Transfer/*genetics
Sequence Alignment
Sequence Homology, Nucleic Acid
Tandem Repeat Sequences

@article {pmid29904051,
year = {2018},
author = {Chen, N and Cai, Y and Chen, Q and Li, R and Wang, K and Huang, Y and Hu, S and Huang, S and Zhang, H and Zheng, Z and Song, W and Ma, Z and Ma, Y and Dang, R and Zhang, Z and Xu, L and Jia, Y and Liu, S and Yue, X and Deng, W and Zhang, X and Sun, Z and Lan, X and Han, J and Chen, H and Bradley, DG and Jiang, Y and Lei, C},
title = {Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2337},
pmid = {29904051},
issn = {2041-1723},
support = {31501918//National Natural Science Foundation of China (National Science Foundation of China)/International ; },
mesh = {Animals ; *Breeding ; Cattle/*genetics ; China ; Chromosomes/ultrastructure ; Domestication ; Female ; Genetic Variation ; *Genetics, Population ; *Genome ; Geography ; Haplotypes ; Male ; Mitochondria ; Models, Statistical ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; Tibet ; },
abstract = {Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6-49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.},
}

Animals
*Breeding
Cattle/*genetics
China
Chromosomes/ultrastructure
Domestication
Female
Genetic Variation
*Genetics, Population
*Genome
Geography
Haplotypes
Male
Mitochondria
Models, Statistical
Phylogeny
Polymorphism, Single Nucleotide
Species Specificity
Tibet

@article {pmid30570818,
year = {2018},
author = {Williams, AM and Friso, G and van Wijk, KJ and Sloan, DB},
title = {Extreme variation in rates of evolution in the plastid Clp protease complex.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.14208},
pmid = {30570818},
issn = {1365-313X},
abstract = {Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multisubunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. The clpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history of clpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that clpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g., loss of introns and RNA-editing sites) within seed plants. Although clpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genus Silene, which has highly elevated and heterogeneous rates of clpP1 evolution. We confirmed that clpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergent Silene species. Additionally, there is a tight correlation between amino-acid substitution rates in clpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting ongoing selection on interactions within this complex. This article is protected by copyright. All rights reserved.},
}

@article {pmid30565720,
year = {2018},
author = {Morsi, M and Kobeissy, F and Magdeldin, S and Maher, A and Aboelmagd, O and Johar, D and Bernstein, L},
title = {A shared comparison of diabetes mellitus and neurodegenerative disorders.},
journal = {Journal of cellular biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcb.28094},
pmid = {30565720},
issn = {1097-4644},
abstract = {Diabetes mellitus (DM), one of the most prevalent metabolic diseases in the world population, is associated with a number of comorbid conditions including obesity, pancreatic endocrine changes, and renal and cardio-cerebrovascular alterations, coupled with peripheral neuropathy and neurodegenerative disease, some of these disorders are bundled into metabolic syndrome. Type 1 DM (T1DM) is an autoimmune disease that destroys the insulin-secreting islet cells. Type 2 DM (T2DM) is diabetes that is associated with an imbalance in the glucagon/insulin homeostasis that leads to the formation of amyloid deposits in the brain, pancreatic islet cells, and possibly in the kidney glomerulus. There are several layers of molecular pathologic alterations that contribute to the DM metabolic pathophysiology and its associated neuropathic manifestations. In this review, we describe the general signature metabolic features of DM and the cross-talk with neurodegeneration. We will assess the underlying molecular key players associated with DM-induced neuropathic disorders that are associated with both T1DM and T2DM. In this context, we will highlight the role of tau and amyloid protein deposits in the brain as well in the pancreatic islet cells, and possibly in the kidney glomerulus. Furthermore, we will discuss the central role of mitochondria, oxidative stress, and the unfolded protein response in mediating the DM-associated neuropathic degeneration. This study will elucidate the relationship between DM and neurodegeneration which may account for the evolution of other neurodegenerative diseases, particularly Alzheimer's disease and Parkinson's disease as discussed later.},
}

@article {pmid30563833,
year = {2018},
author = {Wynn, EL and Christensen, AC},
title = {Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1534/g3.118.200948},
pmid = {30563833},
issn = {2160-1836},
abstract = {Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are not well-conserved between species, and are not always annotated in mitochondrial sequence assemblies. We systematically identified and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find and curate non-tandem repeats larger than 50bp and analyzed the complete mitochondrial sequences from 157 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss. We suggest an adaptive explanation for the existence of the repeats and their evolution.},
}

@article {pmid30563453,
year = {2018},
author = {Harman, A and Barth, C},
title = {The Dictyostelium discoideum homologue of Twinkle, Twm1, is a mitochondrial DNA helicase, an active primase and promotes mitochondrial DNA replication.},
journal = {BMC molecular biology},
volume = {19},
number = {1},
pages = {12},
doi = {10.1186/s12867-018-0114-7},
pmid = {30563453},
issn = {1471-2199},
abstract = {BACKGROUND: DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to also possess primase activity, as has been shown in plants; however this activity appears to have been lost in metazoans. Given this, the study of Twinkle in other organisms is required to better understand the evolution of this family and the roles it performs within mitochondria.

RESULTS: Here we describe the characterization of a Twinkle homologue, Twm1, in the amoeba Dictyostelium discoideum, a model organism for mitochondrial genetics and disease. We show that Twm1 is important for mitochondrial function as it maintains mitochondrial DNA copy number in vivo. Twm1 is a helicase which unwinds DNA resembling open forks, although it can act upon substrates with a single 3' overhang, albeit less efficiently. Furthermore, unlike human Twinkle, Twm1 has primase activity in vitro. Finally, using a novel in bacterio approach, we demonstrated that Twm1 promotes DNA replication.

CONCLUSIONS: We conclude that Twm1 is a replicative mitochondrial DNA helicase which is capable of priming DNA for replication. Our results also suggest that non-metazoan Twinkle could function in the initiation of mitochondrial DNA replication. While further work is required, this study has illuminated several alternative processes of mitochondrial DNA maintenance which might also be performed by the Twinkle family of helicases.},
}

@article {pmid30313490,
year = {2018},
author = {Katoh, TK and Zhang, G and Zhou, CJ and Gao, JJ},
title = {Taxonomy of the Hirtodrosophila melanderi species group (Diptera: Drosophilidae), with descriptions of four new species from southwestern China.},
journal = {Zootaxa},
volume = {4422},
number = {3},
pages = {345-365},
doi = {10.11646/zootaxa.4422.3.2},
pmid = {30313490},
issn = {1175-5334},
mesh = {Animals ; China ; *Diptera ; *Drosophilidae ; Mitochondria ; Phylogeny ; Tibet ; },
abstract = {The Hirtodrosophila melanderi species group contains nine known species recorded from either the Old or the New World. All these species were thought to be strict fungivorous drosophilids. In the present study, we give supplementary descriptions for three of these known species, all recorded from Yunnan, southwestern China, H. furcapenis, H. furcapenisoides, and H. longifurcapenis, by examining respective type specimen(s). We then describe four new species of the same group, H. seticlasper Katoh Gao, sp. nov., H. spinicerca Katoh Gao, sp. nov., H. serratifurcapenis Katoh Gao, sp. nov., and H. truncifurca Katoh Gao, sp. nov., all discovered recently from high altitudes (ca. 3,500 to 3,800 m a.s.l.) in Tibet (Xizang), southwestern China. The delimitation of these new species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI (cytochrome c oxydase, subunits I) gene. In addition, a key to all the species of the species group is provided.},
}

Animals
China
*Diptera
*Drosophilidae
Mitochondria
Phylogeny
Tibet

@article {pmid30213880,
year = {2018},
author = {Ramrath, DJF and Niemann, M and Leibundgut, M and Bieri, P and Prange, C and Horn, EK and Leitner, A and Boehringer, D and Schneider, A and Ban, N},
title = {Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6413},
pages = {},
doi = {10.1126/science.aau7735},
pmid = {30213880},
issn = {1095-9203},
mesh = {*Evolution, Molecular ; Mitochondrial Ribosomes/*chemistry/ultrastructure ; Models, Molecular ; Protozoan Proteins/*chemistry/ultrastructure ; RNA, Ribosomal/chemistry/ultrastructure ; Ribosomal Proteins/*chemistry/ultrastructure ; Trypanosoma brucei brucei/*ultrastructure ; },
abstract = {Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of Trypanosoma brucei, a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.},
}

*Evolution, Molecular
Mitochondrial Ribosomes/*chemistry/ultrastructure
Models, Molecular
Protozoan Proteins/*chemistry/ultrastructure
RNA, Ribosomal/chemistry/ultrastructure
Ribosomal Proteins/*chemistry/ultrastructure
Trypanosoma brucei brucei/*ultrastructure

@article {pmid28903620,
year = {2018},
author = {Kim, IH and Park, J and Suk, HY and Bae, HG and Min, MS and Tsai, TS and Park, D},
title = {Phylogenetic relationships of three representative sea krait species (genus Laticauda; elapidae; serpentes) based on 13 mitochondrial genes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {772-777},
doi = {10.1080/24701394.2017.1357710},
pmid = {28903620},
issn = {2470-1408},
mesh = {Animals ; Biological Evolution ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Elapidae/*genetics ; Genes, Mitochondrial/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Laticauda/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Snakes/genetics ; },
abstract = {To investigate the phylogenetic relationships of the genus Laticauda to related higher taxa, we compared the sequences of four mitochondrial genes (12S rRNA, 16S rRNA, ND4, Cytb) from three Laticauda species (L. colubrina, L. laticaudata, and L. semifasciata) with those of 55 Asian and Australo-Melanesian elapid species. We also characterized the complete mitogenomes of the three Laticauda species and compared the sequences of 13 mitochondrial genes from Laticauda species with five terrestrial elapid and one viperid species to estimate phylogenetic relationships and divergence times. Our results showed that the genus Laticauda is paraphyletic to terrestrial elapids and diverged from the Asian elapids approximately 16.23 Mya. The mitogenomes of the three Laticauda species commonly encoded 13 proteins, 22 tRNAs, 12S and 16S rRNAs and two control regions and ranged from 17,170 and 17,450 bp in size. The L. colubrina mitogenome was more similar to that of L. laticaudata than that of L. semifasciata. The divergence time among the three Laticauda clades was estimated at 8-10 Mya, and a close phylogenetic relationship between L. colubrina and L. laticaudata was found. Our results contribute to our understanding of the evolutionary history of sea kraits.},
}

Animals
Biological Evolution
DNA
DNA Barcoding, Taxonomic/methods
DNA, Mitochondrial/genetics
Elapidae/*genetics
Genes, Mitochondrial/genetics
Genetic Speciation
Genome, Mitochondrial/*genetics
Laticauda/*genetics
Mitochondria/genetics
Phylogeny
RNA, Ribosomal, 16S
Snakes/genetics

@article {pmid28758818,
year = {2018},
author = {Manger, A and Behere, GT and Firake, DM and Sharma, B and Deshmukh, NA and Firake, PD and Azad Thakur, NS and Ngachan, SV},
title = {Genetic characterization of Bactrocera fruit flies (Diptera: Tephritidae) from Northeastern India based on DNA barcodes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {792-799},
doi = {10.1080/24701394.2017.1357713},
pmid = {28758818},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genome, Mitochondrial/genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tephritidae/*genetics ; },
abstract = {The Northeastern region of India, one of the mega biodiversity hot spots has enormous potential for the production of fruits and vegetables. Fruit flies of the genus Bactrocera Macquart are important pests of fruits and vegetables, and one of the limiting factors in successful production of these commodities. The relationship among some of the species is unclear due to their high molecular and morphological similarities. Moreover, due to the significant morphological resemblance between fruit fly species, reliable identification is very difficult task. We genetically characterized 10 fruit fly species of the genus Bactrocera by using standard DNA barcoding region of COI gene. The characterization and identification of eight species were straight forward. This study was unable to establish the molecular identity of Bactrocera sp. 2. Within the 547 bp region of partial COI gene, there were 157 variable sites of which 110 sites were parsimony informative, 153 were synonymous substitutions and 4 were non-synonymous substitutions. The estimate of genetic divergence among the ten species was in the range of 0-21.9% and the pairwise genetic distance of Bactrocera. (Bactrocera) dorsalis (Hendel) with B. (B.) carambolae was only 0.7%. Phylogenetic analysis formed separate clades for fruit and vegetable infesting fruit flies. B. (B.) aethriobasis Hardy, B. (B.) thailandica and B. (B.) tuberculata (Bezzi) have been reported for the first time from the Northeastern India. The information generated from this study would certainly have implications for pest management, taxonomy, quarantine and trade.},
}

Animals
DNA
DNA Barcoding, Taxonomic/methods
DNA, Mitochondrial/*genetics
Electron Transport Complex IV/*genetics
Genetic Speciation
Genome, Mitochondrial/genetics
India
Mitochondria/genetics
Perciformes/genetics
Phylogeny
Sequence Analysis, DNA/methods
Tephritidae/*genetics

@article {pmid28756720,
year = {2018},
author = {Li, YX and Gao, YL and He, XL and Cao, SX},
title = {Exploration of mtDNA control region sequences in Chinese Tibetan Mastiffs.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {800-804},
doi = {10.1080/24701394.2017.1357714},
pmid = {28756720},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Dogs/*genetics ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tibet ; },
abstract = {The control region of mitochondrial DNA (mtDNA) was obtained from 40 purebred Chinese Tibetan Mastiffs (TMs). Sequence structure and genetic diversity were analyzed, and a phylogenetic tree was constructed. The TM mtDNA control region was composed of ETAS (extended termination associated sequences), CD (a central domain) and CSBs (conserved sequenced blocks) and sequence length showed some diversity, which was mainly caused by the number of 10 nucleotide repeat units [5'-GTA CAC GT (G/A) C-3'] between CSB I and CSB II, which ranged from 27 to 35 among individuals. Seventy-five polymorphic sites were identified, which defined 37 haplotypes; the haplotype diversity was 0.990, and the nucleotide diversity was 1.201. Based on the control region sequences, Chinese TMs were divided into three categories, which were consistent with the origin and geographical classification of TMs. Phylogenetic analysis of 538-bp HVR-I sequences revealed that TMs were most closely related to Labrador Retrievers.},
}

Animals
DNA
DNA Barcoding, Taxonomic/methods
DNA, Mitochondrial/*genetics
Dogs/*genetics
Evolution, Molecular
Genetic Speciation
Genetic Variation
Genetics, Population
Genome, Mitochondrial/genetics
Haplotypes
India
Mitochondria/genetics
Perciformes/genetics
Phylogeny
Sequence Analysis, DNA/methods
Tibet

@article {pmid28756717,
year = {2018},
author = {Feng, X and He, D and Sui, X and Chen, Y and Chen, Y},
title = {Morphological and genetic divergence between lake and river populations of Triplophysa in Ngangtse Co, Tibet.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {778-784},
doi = {10.1080/24701394.2017.1357711},
pmid = {28756717},
issn = {2470-1408},
mesh = {Animals ; Biological Evolution ; Cypriniformes/*genetics ; DNA ; DNA, Mitochondrial/genetics ; Ecosystem ; Genetic Drift ; Genetic Speciation ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; Lakes ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Rivers ; Tibet ; },
abstract = {Ngangtse Co (4535 m a.s.l., 840 km2) is a typical endorheic lake in Tibet. In 2015, we investigated the fish resource in this lake and its rivers and collected two Triplophysa species, including T. brevicauda and T. stewarti. To understand the evolutionary dynamics of Triplophysa in Ngangtse Co, the adaptive and genetic divergence between river and lake populations were investigated by analysing their morphological characteristics and mitochondrial COI and Cytb sequences. Among all of 277 samples, the ratios of the number of T. brevicauda to T. stewarti were 27:8, 34:11, 14:24, 37:0, 16:23 and 0:83 in river populations RA, RB, RC, RD, lakeside population LSE and lake population L, respectively. For T. brevicauda, a small but significant genetic divergence (mean FST = 0.0890) was detected between population RD and other three river populations, and significant morphological differences of body length/body height and body length/caudal peduncle length were observed between population RD and RA, RB, suggesting an association between differentiation and geographical distance. For T. stewarti, very high levels of genetic differentiation was observed between population L and other populations with the FST values ranging from 0.4737 (L-RA) to 0.7074 (L-RC). In addition, significant differences of most of morphological characteristics were observed between the lake (L) and river (RC) populations, indicating that lake fish of T. stewarti was a population that showed a long-term adaptation to the saltwater lake. These results provide insights on the evolutionary dynamics of Triplophysa in Ngangtse Co and help us to understand the fish speciation in endorheic lakes on the Qinghai-Tibetan Plateau.},
}

Animals
Biological Evolution
Cypriniformes/*genetics
DNA
DNA, Mitochondrial/genetics
Ecosystem
Genetic Drift
Genetic Speciation
Genetic Variation/genetics
Genome, Mitochondrial/*genetics
Lakes
Microsatellite Repeats
Mitochondria/genetics
Phylogeny
Rivers
Tibet

@article {pmid28752775,
year = {2018},
author = {Wang, ZD and Liao, J and Huang, CQ and Long, SS and Zhang, S and Guo, YS and Liu, L and Liu, CW},
title = {Significant genetic differentiation of Gobiopterus lacustris, a newly recorded transparent goby in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {785-791},
doi = {10.1080/24701394.2017.1357712},
pmid = {28752775},
issn = {2470-1408},
mesh = {Animals ; China ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Drift ; Genetic Variation/genetics ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Philippines ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/methods ; },
abstract = {In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p < .0001) with high haplotype diversity (h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east-west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.},
}

Animals
China
Cyclooxygenase 1/*genetics
DNA Barcoding, Taxonomic/methods
DNA, Mitochondrial/genetics
Gene Flow
Genetic Drift
Genetic Variation/genetics
Genetics, Population
Genome, Mitochondrial/genetics
Haplotypes
Mitochondria/genetics
Perciformes/*genetics
Phenotype
Philippines
Phylogeny
Phylogeography
Sequence Analysis, DNA/methods

@article {pmid28752773,
year = {2018},
author = {Koroiva, R and Kvist, S},
title = {Estimating the barcoding gap in a global dataset of cox1 sequences for Odonata: close, but no cigar.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {765-771},
doi = {10.1080/24701394.2017.1357709},
pmid = {28752773},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We evaluated the extent of intraspecific and interspecific genetic distances for two highly diverse infraorders of Odonata: Anisoptera and Zygoptera. All cytochrome c oxidase subunit I sequences (cox1), the region chosen for zoological DNA barcoding, present in GenBank for each infraorder were downloaded and curated. For Anisoptera, the final dataset consisted of 2,961 individual cox1 sequences for 536 species and the equivalent numbers for Zygoptera were 2,477 sequences for 497 species. More than 7 million individual genetic comparisons were made and the results indicated that there is a tendency towards a barcoding gap, but that the size of the gap may not be sufficient to robustly infer identities for some taxa. DNA barcoding may be of less use for some odonate taxa, perhaps pertaining to misidentifications in global databases. However, at local scales or with more confined taxonomical sampling, this tool may yet be beneficial in identifying these charismatic organisms.},
}

Animals
DNA
DNA Barcoding, Taxonomic/methods
DNA, Mitochondrial/*genetics
Electron Transport Complex IV/*genetics
Genetic Speciation
Genetic Variation
Genome, Mitochondrial/*genetics
Mitochondria/genetics
Odonata/*genetics
Phylogeny
Sequence Analysis, DNA

@article {pmid28745560,
year = {2018},
author = {Bhatti, S and Abbas, S and Aslamkhan, M and Attimonelli, M and Trinidad, MS and Aydin, HH and de Souza, EMS and Gonzalez, GR},
title = {Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {714-726},
doi = {10.1080/24701394.2017.1350951},
pmid = {28745560},
issn = {2470-1408},
mesh = {Adult ; Asian Continental Ancestry Group/genetics ; DNA, Mitochondrial/*genetics ; Ethnic Groups/genetics ; European Continental Ancestry Group/genetics ; Gene Pool ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Pakistan ; Phylogeny ; Phylogeography ; Social Class ; },
abstract = {To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.},
}

Adult
Asian Continental Ancestry Group/genetics
DNA, Mitochondrial/*genetics
Ethnic Groups/genetics
European Continental Ancestry Group/genetics
Gene Pool
Genetic Variation
Genetics, Population/methods
Genome, Mitochondrial/genetics
Haplotypes
Humans
Male
Mitochondria/genetics
Pakistan
Phylogeny
Phylogeography
Social Class

@article {pmid28745537,
year = {2018},
author = {Nakazawa, T and Liu, SV and Sakai, Y and Araki, KS and Tsai, CH and Okuda, N},
title = {Spatial genetic structure and body size divergence in endangered Gymnogobius isaza in ancient Lake Biwa.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {756-764},
doi = {10.1080/24701394.2017.1357708},
pmid = {28745537},
issn = {2470-1408},
mesh = {Animals ; Body Size/*genetics ; DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; Japan ; Lakes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Phylogeny ; },
abstract = {Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait. The results showed that the major lineage dominated all the sampling locations whereas the minor lineage consisted of only 11% (16/143) of samples. Furthermore, although their spatial distributions overlapped (i.e. the two lineages may be well mixed), we found it possible that the minor lineage may have a potentially narrower distribution than the major lineage. In addition, we found that the two lineages differ in body size; specifically, the minor lineage is smaller in size. From the viewpoint of genetic diversity conservation and sustainable resource use, this fish should be managed as two genetic stocks and spatial and/or body size-based fishery management is desirable, with particular attention to the minor (smaller sized) lineage.},
}

Animals
Body Size/*genetics
DNA, Mitochondrial/genetics
Endangered Species
Genetic Variation/genetics
Genome, Mitochondrial/genetics
Japan
Lakes
Mitochondria/genetics
Perciformes/*genetics
Phenotype
Phylogeny

@article {pmid28712321,
year = {2018},
author = {Wang, ZL and Yang, XQ and Wang, TZ and Yu, X},
title = {Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {695-702},
doi = {10.1080/24701394.2017.1350949},
pmid = {28712321},
issn = {2470-1408},
mesh = {Animals ; China ; DNA ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/*genetics ; Farms ; Genetic Speciation ; Genetic Variation ; Genome, Insect/*genetics ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Spiders/*genetics ; },
abstract = {DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.},
}

Animals
China
DNA
DNA Barcoding, Taxonomic/methods
Electron Transport Complex IV/*genetics
Farms
Genetic Speciation
Genetic Variation
Genome, Insect/*genetics
Genome, Mitochondrial
Mitochondria/genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Species Specificity
Spiders/*genetics

@article {pmid28712317,
year = {2018},
author = {Han, CC and Fang, LS and Chang, IM and Lin, HD},
title = {Genetic variation of the land-locked freshwater shrimp Caridina pseudodenticulata (Decapoda: Atyidae: Caridina) in Taiwan.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {687-694},
doi = {10.1080/24701394.2017.1350948},
pmid = {28712317},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Decapoda (Crustacea)/*genetics ; Electron Transport Complex IV/*genetics ; Fresh Water ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; Rivers ; Sequence Analysis, DNA/methods ; Shellfish ; Taiwan ; },
abstract = {Caridina pseudodenticulata is a land-locked freshwater shrimp, which is endemic to North and West Taiwan. It is listed as Vulnerable under criteria A1ce in the IUCN Red List. Our study used mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) gene to examine its genetic structure. In total, 204 sequences were analyzed from 22 populations, and all 39 haplotypes were identified. Our study (1) found that the genetic diversity within population of this species was similar to that of other land-locked freshwater prawn in Taiwan; (2) displayed that during glaciation, the Taiwan Strait was largely above water, an event which created opportunities for colonization Taiwan and dispersal widely; (3) showed that although the phylogenetic analysis showed the lack of a population genetic structure, the AMOVA and haplotypes distribution pattern revealed geographically divided; (4) indicated that C. pseudodenticulata could across to neighbor rivers through the mouths of rivers, which confluent with each other during floods.},
}

Animals
DNA, Mitochondrial/genetics
Decapoda (Crustacea)/*genetics
Electron Transport Complex IV/*genetics
Fresh Water
Genetic Variation
Genetics, Population/methods
Genome, Mitochondrial/genetics
Mitochondria/genetics
Phylogeny
Rivers
Sequence Analysis, DNA/methods
Shellfish
Taiwan

@article {pmid28673190,
year = {2018},
author = {Koç, H and Bülbül, U and Kurnaz, M and İhsan Eroğlu, A and Kutrup, B},
title = {Phylogenetic relationships of Podarcis siculus (Rafinesque-Schmaltz, 1810) and Podarcis tauricus (Pallas, 1814) in Turkey, based on mitochondrial DNA.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {664-673},
doi = {10.1080/24701394.2017.1342245},
pmid = {28673190},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA, Mitochondrial/*genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Lizards/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Turkey ; },
abstract = {The Italian wall lizard and the Balkan wall lizard have a series of taxonomic revisions. However, their phylogenetic relationships still remain uncertain in Turkey. In the present study, we have assessed taxonomic relationships, both of Podarcis siculus and Podarcis tauricus through estimation of phylogenetic relationships among 43 and 42 specimens, respectively, using mtDNA (16 S rRNA and cytb) from great main populations in Turkey. The genetic distances among the populations of P. siculus in Turkey were very low and they were ranged from 0.2 to 1.6% in 16 S rRNA while they were ranged from 0.0% to 3.3% in cytb. On the other hand, the p-distances among the populations of P. tauricus were ranged from 0.0 to 0.6% in 16 S rRNA while they were 0.2% cytb in Turkey. Finally, most of the topologically identical trees of phylogenetic analyses and p-distances showed that monophyly was found in extant populations of P. siculus and P. tauricus. The nominate subspecies, P. s. siculus and P. t. tauricus are representatives of these lizards in Turkey.},
}

Animals
DNA
DNA, Mitochondrial/*genetics
Genetic Speciation
Genome, Mitochondrial/*genetics
Lizards/*genetics
Mitochondria/genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Turkey

@article {pmid28622748,
year = {2018},
author = {Iswarya Deepti, V and Kandula, S and Khedkar, GD},
title = {DNA barcoding of five species of groupers (Pisces: Serranidae) off Visakhapatnam, central eastern coast of India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {659-663},
doi = {10.1080/24701394.2017.1339188},
pmid = {28622748},
issn = {2470-1408},
mesh = {Animals ; Bass/*genetics ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; },
abstract = {Grouper species of Epinephelus - E. epistictus, E. heniochus, E. latifasciatus, E. magniscuttis and E. radiatus exhibit overlapping colour pattern that often leads to misidentification in the field. Even the colour pattern of juveniles of these species in different size groups varies considerably with that of adults. DNA barcoding of these five species was carried out to reinforce our knowledge on existing taxonomic relationships derived based on morphological and biochemical genetic studies that were previously done from Indian waters. Mean interspecific genetic distance is in the range 0.079-0.164.The phylogeny tree revealed distinct clades for species that are in concurrence with previous taxonomic and allozyme electrophoretic studies carried out from central eastern coast of India. Barcode sequences generated for the first time for species E. heniochus from Indian waters for E. magniscuttis so far there are no reference sequences in GenBank.},
}

Animals
Bass/*genetics
DNA
DNA Barcoding, Taxonomic/methods
DNA, Mitochondrial/*genetics
Electron Transport Complex IV/genetics
Genetic Speciation
Genome, Mitochondrial/*genetics
India
Mitochondria/genetics
Perciformes/genetics
Phylogeny

@article {pmid29973152,
year = {2018},
author = {Vanhove, MPM and Briscoe, AG and Jorissen, MWP and Littlewood, DTJ and Huyse, T},
title = {The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae).},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {520},
pmid = {29973152},
issn = {1471-2164},
support = {BR/132/PI/TILAPIA//Federaal Wetenschapsbeleid/ ; GB-TAF-2984//SYNTHESYS/ ; GB-TAF-4940//SYNTHESYS/ ; ZRDC2014MP084//Vlaamse Interuniversitaire Raad/ ; P505/12/G112 (ECIP)//Grantová Agentura České Republiky/ ; K220314N//Fonds Wetenschappelijk Onderzoek/ ; Mbisa Congo project//Belgian Development Cooperation/ ; BOF Reserve Fellowship//Universiteit Hasselt/ ; },
mesh = {Animals ; Cichlids/*parasitology ; DNA, Protozoan/chemistry/isolation & purification/metabolism ; Gene Order ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/classification/*genetics ; Phylogeny ; Platyhelminths/*genetics ; Protozoan Proteins/classification/genetics ; RNA, Ribosomal/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.

RESULTS: Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines.

CONCLUSIONS: The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.},
}

Animals
Cichlids/*parasitology
DNA, Protozoan/chemistry/isolation & purification/metabolism
Gene Order
Genome, Mitochondrial
High-Throughput Nucleotide Sequencing
Mitochondria/classification/*genetics
Phylogeny
Platyhelminths/*genetics
Protozoan Proteins/classification/genetics
RNA, Ribosomal/classification/genetics
Sequence Analysis, DNA

@article {pmid30486096,
year = {2018},
author = {Agarwal, I and Mahony, S and Giri, VB and Chaitanya, R and Bauer, AM},
title = {Six new Cyrtodactylus (Squamata: Gekkonidae) from northeast India.},
journal = {Zootaxa},
volume = {4524},
number = {5},
pages = {501-535},
pmid = {30486096},
issn = {1175-5334},
mesh = {Animals ; *Color ; India ; *Lizards ; Mitochondria ; Myanmar ; Phylogeny ; },
abstract = {We use mitochondrial sequence data to identify divergent lineages within the gekkonid genus Cyrtodactylus in northeast India and use morphological data to describe six new species from within the Indo-Burma clade of Cyrtodactylus. The new species share an irregular colour pattern but differ from described species from the region in morphology and mitochondrial sequence data (>11 % uncorrected pairwise sequence divergence). Three new species are from along the Brahmaputra River and three are from mountains south of the Brahmaputra, including the largest Cyrtodactylus from India and the fifth gecko to be described from a major Indian city, Guwahati.},
}

Animals
*Color
India
*Lizards
Mitochondria
Myanmar
Phylogeny

@article {pmid29855375,
year = {2018},
author = {Amzati, GS and Pelle, R and Muhigwa, JB and Kanduma, EG and Djikeng, A and Madder, M and Kirschvink, N and Marcotty, T},
title = {Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region.},
journal = {Parasites & vectors},
volume = {11},
number = {1},
pages = {329},
pmid = {29855375},
issn = {1756-3305},
support = {ABC089//Africa Biosciences Challenge Fund (ABCF) program, BecA-ILRI Hub/ ; S0020***10402//Agence Universitaire de la Francophonie/ ; IFS-92890CA3//International Foundation for Science/ ; Bourses institutionnelles-Ceruna//Université de Namur/ ; 006/014//Communauté économique des pays des Grands Lacs (CEPGL)/ ; },
mesh = {Africa/epidemiology ; Animals ; Arachnid Vectors/*genetics/parasitology ; Cattle ; Genetic Structures ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; Rhipicephalus/*genetics/parasitology ; Theileria parva/*physiology ; Theileriasis/epidemiology/*parasitology ; },
abstract = {BACKGROUND: The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa.

METHODS: Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution.

RESULTS: Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa.

CONCLUSIONS: Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes.},
}

Africa/epidemiology
Animals
Arachnid Vectors/*genetics/parasitology
Cattle
Genetic Structures
*Genetic Variation
Genetics, Population
Mitochondria/genetics
Phylogeny
Phylogeography
Population Dynamics
Rhipicephalus/*genetics/parasitology
Theileria parva/*physiology
Theileriasis/epidemiology/*parasitology

@article {pmid30545443,
year = {2018},
author = {Son, JM and Lee, C},
title = {Mitochondria and aging.},
journal = {BMB reports},
volume = {},
number = {},
pages = {},
pmid = {30545443},
issn = {1976-670X},
abstract = {Aging is accompanied by a time-dependent progressive deterioration of multiple factors of the cellular system. The past several decades have witnessed major leaps in our understanding of the biological mechanism of aging using dietary, genetic, pharmacological, and physical interventions. Metabolic processes, including nutrient sensing pathways and mitochondrial function, have emerged as prominent regulators of aging. Mitochondria have been considered to play a key role largely due to their production of reactive oxygen species (ROS), resulting in DNA damage that accumulates over time and ultimately causes cellular failure. This theory, known as the mitochondrial free radical theory of aging (MFRTA), was favored by the aging field, but increasing inconsistent evidence has led to criticism and rejection of this idea. However, MFRTA should not be hastily rejected in its entirety because we now understand that ROS is not simply an undesired toxic metabolic byproduct, but also an important signaling molecule that is vital to cellular fitness. Notably, mitochondrial function, a term traditionally referred to bioenergetics and apoptosis, has since expanded considerably. It encompasses numerous other key biological processes, including the following: (i) complex metabolic processes, (ii) intracellular and endocrine signaling/communication, and (iii) immunity/inflammation. Here, we will discuss shortcomings of previous concepts regarding mitochondria in aging and their emerging roles based on recent advances. We will also discuss how the mitochondrial genome integrates with major theories on the evolution of aging.},
}

@article {pmid30285603,
year = {2018},
author = {Chen, G and Zou, Y and Hu, J and Ding, Y},
title = {Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {720},
pmid = {30285603},
issn = {1471-2164},
support = {31471464//National Nature Science Foundation of China/ ; 2013CB126900//"973" Program of China/ ; },
mesh = {Chromosomes, Plant/genetics ; Droughts ; *Gene Expression Profiling ; Genome, Plant/genetics ; *Genomics ; Intracellular Space/metabolism ; MicroRNAs/genetics ; Oryza/drug effects/*genetics/metabolism/*physiology ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Transport ; Salts/pharmacology ; Stress, Physiological/drug effects/*genetics ; Synteny ; },
abstract = {BACKGROUND: Pentatricopeptide-repeat proteins (PPRs) are characterized by tandem arrays of a degenerate 35-amino-acid (PPR motifs), which can bind RNA strands and participate in post-transcription. PPR proteins family is one of the largest families in land plants and play important roles in organelle RNA metabolism and plant development. However, the functions of PPR genes involved in biotic and abiotic stresses of rice (Oryza sativa L.) remain largely unknown.

RESULTS: In the present study, a comprehensive genome-wide analysis of PPR genes was performed. A total of 491 PPR genes were found in the rice genome, of which 246 PPR genes belong to the P subfamily, and 245 genes belong to the PLS subfamily. Gene structure analysis showed that most PPR genes lack intron. Chromosomal location analysis indicated that PPR genes were widely distributed in all 12 rice chromosomes. Phylogenetic relationship analysis revealed the distinct difference between the P and PLS subfamilies. Many PPR proteins are predicted to target chloroplasts or mitochondria, and a PPR protein (LOC_Os10g34310) was verified to localize in mitochondria. Furthermore, three PPR genes (LOC_Os03g17634,LOC_Os07g40820,LOC_Os04g51350) were verified as corresponding miRNA targets. The expression pattern analysis showed that many PPR genes could be induced under biotic and abiotic stresses. Finally, seven PPR genes were confirmed with their expression patterns under salinity or drought stress.

CONCLUSIONS: We found 491 PPR genes in the rice genome, and our genes structure analysis and syntenic analysis indicated that PPR genes might be derived from amplification by retro-transposition. The expression pattern present here suggested that PPR proteins have crucial roles in response to different abiotic stresses in rice. Taken together, our study provides a comprehensive analysis of the PPR gene family and will facilitate further studies on their roles in rice growth and development.},
}

Chromosomes, Plant/genetics
Droughts
*Gene Expression Profiling
Genome, Plant/genetics
*Genomics
Intracellular Space/metabolism
MicroRNAs/genetics
Oryza/drug effects/*genetics/metabolism/*physiology
Phylogeny
Plant Proteins/*genetics/metabolism
Protein Transport
Salts/pharmacology
Stress, Physiological/drug effects/*genetics
Synteny

@article {pmid30535838,
year = {2018},
author = {Kumar, V and Santhosh Kumar, TR and Kartha, CC},
title = {Mitochondrial membrane transporters and metabolic switch in heart failure.},
journal = {Heart failure reviews},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10741-018-9756-2},
pmid = {30535838},
issn = {1573-7322},
abstract = {Mitochondrial dysfunction is widely recognized as a major factor for the progression of cardiac failure. Mitochondrial uptake of metabolic substrates and their utilization for ATP synthesis, electron transport chain activity, reactive oxygen species levels, ion homeostasis, mitochondrial biogenesis, and dynamics as well as levels of reactive oxygen species in the mitochondria are key factors which regulate mitochondrial function in the normal heart. Alterations in these functions contribute to adverse outcomes in heart failure. Iron imbalance and oxidative stress are also major factors for the evolution of cardiac hypertrophy, heart failure, and aging-associated pathological changes in the heart. Mitochondrial ATP-binding cassette (ABC) transporters have a key role in regulating iron metabolism and maintenance of redox status in cells. Deficiency of mitochondrial ABC transporters is associated with an impaired mitochondrial electron transport chain complex activity, iron overload, and increased levels of reactive oxygen species, all of which can result in mitochondrial dysfunction. In this review, we discuss the role of mitochondrial ABC transporters in mitochondrial metabolism and metabolic switch, alterations in the functioning of ABC transporters in heart failure, and mitochondrial ABC transporters as possible targets for therapeutic intervention in cardiac failure.},
}

@article {pmid30527196,
year = {2018},
author = {Kazdal, D and Harms, A and Endris, V and Penzel, R and Oliveira, C and Kriegsmann, M and Longuespée, R and Winter, H and Schneider, MA and Muley, T and Pfarr, N and Weichert, W and Stenzinger, A and Warth, A},
title = {Subclonal evolution of pulmonary adenocarcinomas delineated by spatially distributed somatic mitochondrial mutations.},
journal = {Lung cancer (Amsterdam, Netherlands)},
volume = {126},
number = {},
pages = {80-88},
doi = {10.1016/j.lungcan.2018.10.024},
pmid = {30527196},
issn = {1872-8332},
abstract = {OBJECTIVES: The potential role of cancer associated somatic mutations of the mitochondrial genome (mtDNA) is controversial and still poorly understood. Our group and others recently challenged a direct tumorigenic impact and suggested a passenger-like character. In combination with the known increased mutation rate, somatic mtDNA mutations account for an interesting tool to delineate tumor evolution. Here, we comprehensively analyzed the spatial distribution of somatic mtDNA mutations throughout whole tumor sections of pulmonary adenocarcinoma (ADC).

MATERIALS AND METHODS: Central sections of 19 ADC were analyzed in a segmented manner (11-34 segments/tumor) together with non-neoplastic tissue samples and lymph node metastasis, if present. We performed whole mtDNA sequencing and real-time PCR based quantification of mtDNA copy numbers for all samples. Further, histological growth patterns were determined on H&E sections and the tumor cell content was quantified by digital pathology analyses.

RESULTS: Somatic mtDNA mutations were present in 96% (18/19) of the analyzed tumors, either ubiquitously or restricted to specific tumor regions. Spatial and histological mapping of the mutations enabled the identification of subclonal structures and phylogenetic relations within a tumor section indicating different progression levels. In this regard, lymph node metastases seem to be related to early events in ADC development. There was no concurrence between histological and mtDNA mutation based clusters. However, micropapillary patterns occurred only in tumors with ubiquitous mutations. ADC with more than two ubiquitous mutations were associated with shorter disease-free survival (p < 0.01).

CONCLUSION: Cancer related mtDNA mutations are interesting candidates for the understanding of subclonal ADC evolution and perspectively for monitoring tumor progression. Our data reveal a potential prognostic relevance of somatic mtDNA mutations.},
}

@article {pmid30343708,
year = {2018},
author = {Tanaka, A and Leung, PSC and Gershwin, ME},
title = {Evolution of our understanding of PBC.},
journal = {Best practice & research. Clinical gastroenterology},
volume = {34-35},
number = {},
pages = {3-9},
doi = {10.1016/j.bpg.2018.05.008},
pmid = {30343708},
issn = {1532-1916},
mesh = {Animals ; Autoantibodies/blood ; Autoantigens/immunology ; Epitopes ; Humans ; Liver Cirrhosis, Biliary/*immunology/*pathology ; Mitochondria/immunology ; },
abstract = {The discovery of mitochondrial autoantigens recognized by antimitochondrial antibodies (AMAs) in 1987 marked the dawn of a new era in primary biliary cholangitis (PBC) research. Since then, there has been substantial progress in our understanding of PBC partly bestowed by the development of innovative technologies in molecular biology, immunology, and genetics. Here, we review this evolutionary progress in understanding PBC. We now recognize that the epitopes of AMAs, CD4+, and CD8+ T cells are all mapped to the same region of the inner lipoyl domain of pyruvate dehydrogenase complex E2 subunit (PDC-E2), and that intrahepatic biliary epithelial cells (BECs) are exclusively targeted in PBC. BECs express PDC-E2 on apotopes in an immunologically intact form during apoptosis, but not other epithelial cells, which could explain the tissue specificity of PBC. In addition, genetic factors, environmental triggers, and epigenetic modifications play crucial roles in the development of PBC. Intact lipoylated PDC-E2, presumably after modification with xenobiotics such as 2-octynamide or 2-nonyamide that are abundantly present in the environment, is endocytosed by antigen-presenting cells and are presented to CD4+ or CD8+ T cells. An immune complex consisting of PDC-E2 and anti-PDC-E2 autoantibodies cross-present autoantigens in a more efficient manner. Finally, an adenylate uridine-rich element (ARE) Del -/- mouse model has been established, which presents a disease modeling human PBC, including female dominance as one of its most important features, and can be used to dissect the immunopathology of PBC. Expanding our knowledge of the pathology from a very early stage of the disease will provide the key to cure PBC.},
}

Animals
Autoantibodies/blood
Autoantigens/immunology
Epitopes
Humans
Liver Cirrhosis, Biliary/*immunology/*pathology
Mitochondria/immunology

@article {pmid30309500,
year = {2018},
author = {Miquel, J and Poonlaphdecha, S and Ribas, A},
title = {Spermatological characteristics of the family Glypthelminthidae (Digenea, Plagiorchioidea) inferred from the ultrastructural study of Glypthelmins staffordi Tubangui, 1928.},
journal = {Tissue & cell},
volume = {54},
number = {},
pages = {114-119},
doi = {10.1016/j.tice.2018.08.013},
pmid = {30309500},
issn = {1532-3072},
mesh = {Animals ; Male ; Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/*classification/*ultrastructure ; },
abstract = {The present study describes the ultrastructural organization of the mature spermatozoon of the digenean Glypthelmins staffordi (Glypthelminthidae) by means of transmission electron microscopy. Live digeneans were collected from the Chinese edible frog (Hoplobatrachus rugulosus) in Udon Thani Province (Thailand). The ultrastructural study reveals that the mature spermatozoon of G. staffordi is a filiform cell, which is tapered at both extremities. It exhibits the Bakhoum et al.'s type IV of spermatozoon of digeneans characterized by the 9+'1' axonemes of trepaxonematan Platyhelminthes, the presence of the association "external ornamentation-cortical microtubules", the external ornamentation located in the posterior part of the anterior region, the arrangement of parallel cortical microtubules in two bundles and with its maximum number located in the anterior part of the sperm cell, and the presence of two mitochondria. Other characteristics are the presence of spine-like bodies, a posterior extremity containing only the nucleus, and the presence of a large amount of glycogen granules. Results of the present study are particularly compared with the existing data in other families of the Plagiorchioidea, namely the Brachycoeliidae, the Haematoloechidae, the Omphalometridae and the Plagiorchiidae.},
}

Animals
Male
Phylogeny
Spermatozoa/*ultrastructure
Trematoda/*classification/*ultrastructure

@article {pmid30158483,
year = {2018},
author = {Kozieł, E and Otulak-Kozieł, K and Bujarski, JJ},
title = {Ultrastructural Analysis of Prune DwarfVirus Intercellular Transport and Pathogenesis.},
journal = {International journal of molecular sciences},
volume = {19},
number = {9},
pages = {},
pmid = {30158483},
issn = {1422-0067},
support = {505-10-011100-Q00190-99//Warsaw Univeristy of Life Sciences WULS-SGGW/ ; },
mesh = {Alfalfa mosaic virus/genetics/*pathogenicity/*ultrastructure ; Biological Transport/genetics/physiology ; Phylogeny ; RNA, Viral ; Viral Proteins/metabolism/ultrastructure ; },
abstract = {Prune dwarf virus (PDV) is an important viral pathogen of plum, sweet cherry, peach, and many herbaceous test plants. Although PDV has been intensively investigated, mainly in the context of phylogenetic relationship of its genes and proteins, many gaps exist in our knowledge about the mechanism of intercellular transport of this virus. The aim of this work was to investigate alterations in cellular organelles and the cell-to-cell transport of PDV in Cucumis sativus cv. Polan at ultrastructural level. To analyze the role of viral proteins in local transport, double-immunogold assays were applied to localize PDV coat protein (CP) and movement protein (MP). We observe structural changes in chloroplasts, mitochondria, and cellular membranes. We prove that PDV is transported as viral particles via MP-generated tubular structures through plasmodesmata. Moreover, the computer-run 3D modeling reveals structural resemblances between MPs of PDV and of Alfalfa mosaic virus (AMV), implying similarities of transport mechanisms for both viruses.},
}

Alfalfa mosaic virus/genetics/*pathogenicity/*ultrastructure
Biological Transport/genetics/physiology
Phylogeny
RNA, Viral
Viral Proteins/metabolism/ultrastructure

@article {pmid30032461,
year = {2018},
author = {Sylvester, C and Krishna, MS and Rao, JS and Chandrasekar, A},
title = {Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India.},
journal = {Genetica},
volume = {146},
number = {4-5},
pages = {383-389},
pmid = {30032461},
issn = {1573-6857},
mesh = {Asian Continental Ancestry Group/genetics ; DNA, Mitochondrial/*genetics ; Ethnic Groups/*genetics ; Female ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Humans ; India/ethnology ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The subsequent human migrations that dispersed out of Africa, both prehistoric and historic and colonization of India by modern humans is unanimous, and phylogeny of major mitochondrial DNA haplogroups have played a key role in assessing the genetic origin of people of India. To address more such events, complete mitogenomes of 113 Melakudiya tribe of Southern India were sequenced and 46 individuals showed the presence of west Eurasian autochthonous haplogroups HV14 and U7. Phylogenetic analysis revealed two novel subclades HV14a1b and HV14a1b1 and sequences representing haplogroup U7 were included under previously described subclade U7a3a1a2* specific to India. Moreover, the present analysis on complete mtDNA reveals addition information of the spread and distribution of west Eurasian haplogroups in southern India, in tracing an unexplored genetic link between Melakudiya tribe with the people of Iranian Plateau, South Caucasus, and Central Asia. Coalescence ages of HV14 and U7a3a1a2* trees in the present study dates ~ 16.1 ± 4.3 and ~ 13.4 ± 5.6 kya respectively.},
}

Asian Continental Ancestry Group/genetics
DNA, Mitochondrial/*genetics
Ethnic Groups/*genetics
Female
Genetic Variation/genetics
Genetics, Population/methods
Genome, Mitochondrial/*genetics
Haplotypes/genetics
Humans
India/ethnology
Male
Mitochondria/genetics
Phylogeny
Phylogeography/methods
Sequence Analysis, DNA/methods

@article {pmid29902489,
year = {2018},
author = {Uzarska, MA and Przybyla-Toscano, J and Spantgar, F and Zannini, F and Lill, R and Mühlenhoff, U and Rouhier, N},
title = {Conserved functions of Arabidopsis mitochondrial late-acting maturation factors in the trafficking of iron‑sulfur clusters.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {1865},
number = {9},
pages = {1250-1259},
doi = {10.1016/j.bbamcr.2018.06.003},
pmid = {29902489},
issn = {0167-4889},
mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cloning, Molecular ; DNA-Binding Proteins/genetics/metabolism ; Evolution, Molecular ; Iron/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*growth & development ; Sulfur/metabolism ; },
abstract = {Numerous proteins require iron‑sulfur (Fe-S) clusters as cofactors for their function. Their biogenesis is a multi-step process occurring in the cytosol and mitochondria of all eukaryotes and additionally in plastids of photosynthetic eukaryotes. A basic model of Fe-S protein maturation in mitochondria has been obtained based on studies achieved in mammals and yeast, yet some molecular details, especially of the late steps, still require investigation. In particular, the late-acting biogenesis factors in plant mitochondria are poorly understood. In this study, we expressed the factors belonging to NFU, BOLA, SUFA/ISCA and IBA57 families in the respective yeast mutant strains. Expression of the Arabidopsis mitochondrial orthologs was usually sufficient to rescue the growth defects observed on specific media and/or to restore the abundance or activity of the defective Fe-S or lipoic acid-dependent enzymes. These data demonstrate that the plant mitochondrial counterparts, including duplicated isoforms, likely retained their ancestral functions. In contrast, the SUFA1 and IBA57.2 plastidial isoforms cannot rescue the lysine and glutamate auxotrophies of the respective isa1-isa2Δ and iba57Δ strains or of the isa1-isa2-iba57Δ triple mutant when expressed in combination. This suggests a specialization of the yeast mitochondrial and plant plastidial factors in these late steps of Fe-S protein biogenesis, possibly reflecting substrate-specific interactions in these different compartments.},
}

Arabidopsis/genetics/*metabolism
Arabidopsis Proteins/genetics/*metabolism
Cloning, Molecular
DNA-Binding Proteins/genetics/metabolism
Evolution, Molecular
Iron/metabolism
Mitochondria/genetics/metabolism
Mitochondrial Proteins/genetics/*metabolism
Saccharomyces cerevisiae/genetics/*growth & development
Sulfur/metabolism

@article {pmid29902241,
year = {2018},
author = {Yoshino, H and Yamaji, F and Ohsawa, TA},
title = {Genetic structure and dispersal patterns in Limnoria nagatai (Limnoriidae, Isopoda) dwelling in non-buoyant kelps, Eisenia bicyclis and E. arborea, in Japan.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0198451},
pmid = {29902241},
issn = {1932-6203},
mesh = {Animals ; Demography ; Electron Transport Complex IV/*genetics ; Gene Flow ; Isopoda/*classification/physiology ; Japan ; Kelp/*classification/physiology ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; },
abstract = {The marine isopod genus Limnoria contains algae-eating species. Previous phylogeographic studies have suggested that Limnoria species feeding on buoyant kelp underwent low genetic differentiation on a large spatial scale because rafting on floating host kelps promotes high levels of gene flow. In this paper, we survey the genetic structure of Limnoria nagatai, which bores into the non-buoyant kelps Eisenia bicyclis and E. arborea. We analyze the mitochondrial DNA (cytochrome oxidase subunit I [COI] gene) and morphological traits of L. nagatai, and the host kelps E. bicyclis and E. arborea from 14 populations along the Japanese archipelago of the Pacific Ocean and the Sea of Japan. Four major lineages are recognized within L. nagatai: three lineages in the Pacific Ocean, and one lineage in the Sea of Japan which might be a cryptic species. For L. nagatai, we show high genetic differentiation between geographically separated habitats in the Pacific Ocean, while low differentiation is found among continuous host kelps habitats in the Pacific Ocean as well as the Sea of Japan. L. nagatai in E. bicyclis in the Pacific Ocean has experienced large population expansion after the Last Glacial Maximum (LGM), whereas the lineage in E. bicyclis in the Sea of Japan has not. We suggest that Limnoria feeding on non-buoyant kelps, may attain low genetic differentiation because they might be able to disperse long distance if the habitat of host kelps is continuous. The historical events affecting Limnoria after the LGM may differ between the coasts of the Pacific Ocean and the Sea of Japan.},
}

Animals
Demography
Electron Transport Complex IV/*genetics
Gene Flow
Isopoda/*classification/physiology
Japan
Kelp/*classification/physiology
Mitochondria/genetics
Pacific Ocean
Phylogeny
Phylogeography
Sequence Analysis, DNA/*methods

@article {pmid29880721,
year = {2018},
author = {Zhang, H and Burr, SP and Chinnery, PF},
title = {The mitochondrial DNA genetic bottleneck: inheritance and beyond.},
journal = {Essays in biochemistry},
volume = {62},
number = {3},
pages = {225-234},
doi = {10.1042/EBC20170096},
pmid = {29880721},
issn = {1744-1358},
support = {101876/Z/13/Z//Wellcome Trust/United Kingdom ; MC_UP_1501/2//Medical Research Council/United Kingdom ; G0601943//Medical Research Council/United Kingdom ; },
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene-Environment Interaction ; Genetic Drift ; *Genetic Predisposition to Disease ; Humans ; Mitochondria/physiology ; Organelle Biogenesis ; Selection, Genetic ; },
abstract = {mtDNA is a multicopy genome. When mutations exist, they can affect a varying proportion of the mtDNA present within every cell (heteroplasmy). Heteroplasmic mtDNA mutations can be maternally inherited, but the proportion of mutated alleles differs markedly between offspring within one generation. This led to the genetic bottleneck hypothesis, explaining the rapid changes in allele frequency seen during transmission from one generation to the next. Although a physical reduction in mtDNA has been demonstrated in several species, a comprehensive understanding of the molecular mechanisms is yet to be revealed. Several questions remain, including the role of selection for and against specific alleles, whether all bottlenecks are the same, and precisely how the bottleneck is controlled during development. Although originally thought to be limited to the germline, there is evidence that bottlenecks exist in other cell types during development, perhaps explaining why different tissues in the same organism contain different levels of mutated mtDNA. Moreover, tissue-specific bottlenecks may occur throughout life in response to environmental influences, adding further complexity to the situation. Here we review key recent findings, and suggest ways forward that will hopefully advance our understanding of the role of mtDNA in human disease.},
}

Animals
DNA, Mitochondrial/*genetics
Gene-Environment Interaction
Genetic Drift
*Genetic Predisposition to Disease
Humans
Mitochondria/physiology
Organelle Biogenesis
Selection, Genetic

@article {pmid29618317,
year = {2018},
author = {Doyle, JM and Bell, DA and Bloom, PH and Emmons, G and Fesnock, A and Katzner, TE and LaPré, L and Leonard, K and SanMiguel, P and Westerman, R and Andrew DeWoody, J},
title = {New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus).},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {233},
pmid = {29618317},
issn = {1471-2164},
support = {L12AC20102, L11PX02237, L12AC2010//U.S. Bureau of Land Management/ ; University Faculty Scholar program//Provost's Office at Purdue University/ ; PINN645-21//National Park Service/ ; BIO170038//XSEDE/ ; },
mesh = {Animals ; Avian Proteins/*genetics ; California ; Falconiformes/*classification/genetics ; Female ; Genetics, Population ; Idaho ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*veterinary ; },
abstract = {BACKGROUND: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species' range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.

RESULTS: We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.

CONCLUSIONS: Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California's prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.},
}

Animals
Avian Proteins/*genetics
California
Falconiformes/*classification/genetics
Female
Genetics, Population
Idaho
Mitochondria/genetics
Phylogeny
Phylogeography
*Polymorphism, Single Nucleotide
Whole Genome Sequencing/*veterinary

@article {pmid29476907,
year = {2018},
author = {Layton, KKS and Gosliner, TM and Wilson, NG},
title = {Flexible colour patterns obscure identification and mimicry in Indo-Pacific Chromodoris nudibranchs (Gastropoda: Chromodorididae).},
journal = {Molecular phylogenetics and evolution},
volume = {124},
number = {},
pages = {27-36},
doi = {10.1016/j.ympev.2018.02.008},
pmid = {29476907},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/genetics ; Gastropoda/genetics/*physiology ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Molecular Mimicry/*genetics ; Phylogeny ; Pigmentation/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Chromodoris is a genus of colourful nudibranchs that feed on sponges and is found across the Indo-Pacific. While this was once the most diverse chromodorid genus, recent work has shown that the genus should be restricted to a monophyletic lineage that contains only 22 species, all of which exhibit black pigmentation and planar spawning behaviour. Earlier phylogenies of this group are poorly resolved and thus additional work is needed to clarify species boundaries within Chromodoris. This study presents a maximum-likelihood phylogeny based on mitochondrial loci (COI, 16S) for 345 Chromodoris specimens, including data from 323 new specimens and 22 from GenBank, from across the Indo-Pacific. Species hypotheses and phylogenetic analysis uncovered 39 taxa in total containing 18 undescribed species, with only five of 39 taxa showing stable colour patterns and distinct morphotypes. This study also presents the first evidence for regional mimicry in this genus, with C. colemani and C. joshi displaying geographically-based variation in colour patterns which appear to match locally abundant congenerics, highlighting the flexibility of these colour patterns in Chromodoris nudibranchs. The current phylogeny contains short branch lengths, polytomies and poor support at interior nodes, which is indicative of a recent radiation. As such, future work will employ a transcriptome-based exon capture approach for resolving the phylogeny of this group. In all, this study included 21 of the 22 described species in the Chromodoris sensu stricto group with broad sampling coverage from across the Indo-Pacific, constituting the most comprehensive sampling of this group to date. This work highlights several cases of undocumented diversity, ultimately expanding our knowledge of species boundaries in this group, while also demonstrating the limitations of colour patterns for species identification in this genus.},
}

Animals
Biodiversity
DNA, Mitochondrial/genetics
Gastropoda/genetics/*physiology
Geography
Likelihood Functions
Mitochondria/genetics
Molecular Mimicry/*genetics
Phylogeny
Pigmentation/*genetics
Sequence Analysis, DNA
Species Specificity

@article {pmid29358597,
year = {2018},
author = {Eimanifar, A and Kimball, RT and Braun, EL and Ellis, JD},
title = {Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1333},
pmid = {29358597},
issn = {2045-2322},
mesh = {Animals ; Bees/*classification/cytology/genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Introduced Species ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; South Africa ; },
abstract = {Apis mellifera capensis Eschscholtz and A.m. scutellata Lepeletier are subspecies of western honey bees that are indigenous to the Republic of South Africa (RSA). Both subspecies have invasive potential and are organisms of concern for areas outside their native range, though they are important bees to beekeepers, agriculture, and the environment where they are native. The aim of the present study was to examine genetic differentiation among these subspecies and estimate their phylogenetic relationships using complete mitochondrial genomes sequences. We used 25 individuals that were either assigned to one of the subspecies or designated hybrids using morphometric analyses. Phylogenetic analyses of mitogenome sequences by maximum likelihood (ML) and Bayesian inference identified a monophyletic RSA clade, subdivided into two clades. A haplotype network was consistent with the phylogenetic trees. However, members of both subspecies occurred in both clades, indicating that A.m. capensis and A.m. scutellata are neither reciprocally monophyletic nor do they exhibit paraphyly with one subspecies nested within the other subspecies. Furthermore, no mitogenomic features were diagnostic to either subspecies. All bees analyzed from the RSA expressed a substantial level of haplotype diversity (most samples had unique haplotypes) but limited nucleotide diversity. The number of variable codons across protein-coding genes (PCGs) differed among loci, with CO3 exhibiting the most variation and ATP6 the least.},
}

Animals
Bees/*classification/cytology/genetics
Evolution, Molecular
Genetic Variation
*Genome, Mitochondrial
Haplotypes
Introduced Species
Mitochondria/*genetics
Phylogeny
Sequence Analysis, DNA/*methods
South Africa

@article {pmid28989067,
year = {2018},
author = {Ogedengbe, ME and El-Sherry, S and Ogedengbe, JD and Chapman, HD and Barta, JR},
title = {Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa).},
journal = {International journal for parasitology},
volume = {48},
number = {1},
pages = {59-69},
doi = {10.1016/j.ijpara.2017.07.008},
pmid = {28989067},
issn = {1879-0135},
mesh = {Animals ; Cell Nucleus/*genetics/metabolism ; DNA, Protozoan/*genetics/metabolism ; DNA, Ribosomal/*genetics/metabolism ; Eimeria/classification/*genetics/growth & development/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/*genetics/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences. Although alignment of the mt COI sequences was unambiguous, substitution saturation was evident for comparisons of COI sequences between ingroup (eimeriid) and outgroup (sarcocystid) taxa. Consequently, a combined dataset applying partition-specific analytical and alignment improvements was used to generate a robust molecular phylogeny. Most eimeriid parasites that infect closely related definitive hosts were found in close proximity on the resulting tree, frequently in a single clade. Whether this represents coevolution or co-accommodation or a combination remains an open point. Unlike host associations, basic oocyst configuration (number of sporocysts per oocyst and sporozoites per sporocyst) was not correlated with phylogeny. Neither 'Eimeria-type' nor 'Isospora-type' oocyst morphotypes formed monophyletic groups. In the combined dataset tree (representing only a tiny fraction of described eimeriid coccidia), at least 10 clades of Eimeria spp. would need to be re-assigned to nine distinct genera to resolve their paraphyly. The apparent lack of congruence between morphotype and genotype will require taxonomists to balance nomenclatural stability and diagnostic ease against the ideal of monophyletic genera. For now, recognition of paraphyletic eimeriid genera defined by basic oocyst configuration may be necessary for reasons of taxonomic stability and diagnostic utility. Future taxonomic revisions to produce monophyletic eimeriid genera will ultimately require the identification of reliable phenotypic characters that agree with the molecular phylogeny of these parasites or, less optimally, acceptance that genotyping may be needed to support monophyletic supraspecific taxonomic groups.},
}

Animals
Cell Nucleus/*genetics/metabolism
DNA, Protozoan/*genetics/metabolism
DNA, Ribosomal/*genetics/metabolism
Eimeria/classification/*genetics/growth & development/metabolism
Electron Transport Complex IV/genetics/metabolism
Mitochondria/*genetics/metabolism
*Phylogeny
Sequence Analysis, DNA

@article {pmid28487526,
year = {2017},
author = {Wang, P and Sha, T and Zhang, Y and Cao, Y and Mi, F and Liu, C and Yang, D and Tang, X and He, X and Dong, J and Wu, J and Yoell, S and Yoell, L and Zhang, KQ and Zhang, Y and Xu, J},
title = {Frequent heteroplasmy and recombination in the mitochondrial genomes of the basidiomycete mushroom Thelephora ganbajun.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {1626},
pmid = {28487526},
issn = {2045-2322},
mesh = {Agaricales/*genetics/isolation & purification ; Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Gene Amplification ; Genetic Loci ; *Genome, Mitochondrial ; Geography ; Heterozygote ; Homozygote ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {In the majority of sexual eukaryotes, the mitochondrial genomes are inherited uniparentally. As a result, individual organisms are homoplasmic, containing mitochondrial DNA (mtDNA) from a single parent. Here we analyzed the mitochondrial genotypes in Clade I of the gourmet mushroom Thelephora ganbajun from its broad geographic distribution range. A total of 299 isolates from 28 geographic locations were sequenced at three mitochondrial loci: the mitochondrial small ribosomal RNA gene, and the cytochrome c oxidase subunits I (COX1) and III (COX3) genes. Quantitative PCR analyses showed that the strains had about 60-160 copies of mitochondrial genomes per cell. Interestingly, while no evidence of heteroplasmy was found at the 12S rRNA gene, 262 of the 299 isolates had clear evidence of heterogeneity at either the COX1 (261 isolates) or COX3 (12 isolates) gene fragments. The COX1 heteroplasmy was characterized by two types of introns residing at different sites of the same region and at different frequencies among the isolates. Allelic association analyses of the observed mitochondrial polymorphic nucleotide sites suggest that mtDNA recombination is common in natural populations of this fungus. Our results contrast the prevailing view that heteroplasmy, if exists, is only transient in basidiomycete fungi.},
}

Agaricales/*genetics/isolation & purification
Amino Acid Sequence
Base Sequence
DNA, Mitochondrial/genetics
Electron Transport Complex IV/genetics
Gene Amplification
Genetic Loci
*Genome, Mitochondrial
Geography
Heterozygote
Homozygote
Mitochondria/genetics
Phylogeny
RNA, Ribosomal/genetics
*Recombination, Genetic
Sequence Analysis, DNA

@article {pmid30518034,
year = {2018},
author = {Derbikova, K and Kuzmenko, A and Levitskii, S and Klimontova, M and Chicherin, I and Baleva, MV and Krasheninnikov, IA and Kamenski, P},
title = {Biological and Evolutionary Significance of Terminal Extensions of Mitochondrial Translation Initiation Factor 3.},
journal = {International journal of molecular sciences},
volume = {19},
number = {12},
pages = {},
doi = {10.3390/ijms19123861},
pmid = {30518034},
issn = {1422-0067},
support = {17-14-01005//Russian Science Foundation/ ; 17-54-16005//Russian Foundation for Basic Research/ ; State Assignment AAAA_A16_116021660073_5//Russian Federation Government/ ; },
abstract = {Protein biosynthesis in mitochondria is organized in a bacterial manner. However, during evolution, mitochondrial translation mechanisms underwent many organelle-specific changes. In particular, almost all mitochondrial translation factors, being orthologous to bacterial proteins, are characterized by some unique elements of primary or secondary structure. In the case of the organellar initiation factor 3 (IF3), these elements are several dozen amino acids long N- and C-terminal extensions. This study focused on the terminal extensions of baker's yeast mitochondrial IF3, Aim23p. By in vivo deletion and complementation analysis, we show that at least one extension is necessary for Aim23p function. At the same time, human mitochondrial IF3 is fully functional in yeast mitochondria even without both terminal extensions. While Escherichia coli IF3 itself is poorly active in yeast mitochondria, adding Aim23p terminal extensions makes the resulting chimeric protein as functional as the cognate factor. Our results show that the terminal extensions of IF3 have evolved as the "adaptors" that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.},
}

@article {pmid30517740,
year = {2018},
author = {Petrov, AS and Wood, EC and Bernier, CR and Norris, AM and Brown, A and Amunts, A},
title = {Structural Patching Fosters Divergence of Mitochondrial Ribosomes.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msy221},
pmid = {30517740},
issn = {1537-1719},
abstract = {Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are "patched" by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.},
}

@article {pmid30484227,
year = {2018},
author = {Trosko, JE},
title = {The Role of the Mitochondria in the Evolution of Stem Cells, Including MUSE Stem Cells and Their Biology.},
journal = {Advances in experimental medicine and biology},
volume = {1103},
number = {},
pages = {131-152},
doi = {10.1007/978-4-431-56847-6_7},
pmid = {30484227},
issn = {0065-2598},
abstract = {From the transition of single-cell organisms to multicellularity of metazoans, evolutionary pressures selected new genes and phenotypes to cope with the oxygenation of the Earth's environment, especially via the symbiotic acquisition of the mitochondrial organelle. There were many new genes and phenotypes that appeared, namely, stem cells, low-oxygen-micro-environments to house these genes ("niches"), new epigenetic mechanisms to regulate , selectively, the gene repertoire to control proliferation, differentiation, apoptosis, senescence and DNA protection mechanisms, including antioxidant genes and DNA repair. This transition required a critical regulation of the metabolism of glucose to produce energy for both the stem cell quiescent state and the energy-requiring differentiated state. While the totipotent-, embryonic-, pluripotent-, and a few adult organ-specific stem cells were recognized, only relatively recently, because of the isolation of somatic cell nuclear transfer (SCNT) stem cells and "induced pluripotent stem" cells, challenges to the origin of these "iPS" cells have been made. The isolation and characterization of human MUSE stem cells and more adult organ-specific adult stem cells have indicated that these MUSE cells have many shared characteristics of the "iPS" cells, yet they do not form teratomas but can give rise to the trigeminal cell layers. While the MUSE cells are a subset of human fibroblastic cells, they have not been characterized, yet, for the mitochondrial metabolic genes, either in the stem cell state or during their differentiation processes. A description of other human adult stem cells will be made to set future studies of how the MUSE stem cells compare to all other stem cells.},
}

@article {pmid30481564,
year = {2018},
author = {Xie, B and Wang, S and Jiang, N and Li, JJ},
title = {Cyclin B1/CDK1-regulated mitochondrial bioenergetics in cell cycle progression and tumor resistance.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.canlet.2018.11.019},
pmid = {30481564},
issn = {1872-7980},
abstract = {A mammalian cell houses two genomes located separately in the nucleus and mitochondria. During evolution, communications and adaptations between these two genomes occur extensively to achieve and sustain homeostasis for cellular functions and regeneration. Mitochondria provide the major cellular energy and contribute to gene regulation in the nucleus, whereas more than 98% of mitochondrial proteins are encoded by the nuclear genome. Such two-way signaling traffic presents an orchestrated dynamic between energy metabolism and consumption in cells. Recent reports have elucidated the way how mitochondrial bioenergetics synchronizes with the energy consumption for cell cycle progression mediated by cyclin B1/CDK1 as the communicator. This review is to recapitulate cyclin B1/CDK1 mediated mitochondrial activities in cell cycle progression and stress response as well as its potential link to reprogram energy metabolism in tumor adaptive resistance. Cyclin B1/CDK1-mediated mitochondrial bioenergetics is applied as an example to show how mitochondria could timely sense the cellular fuel demand and then coordinate ATP output. Such nucleus-mitochondria oscillation may play key roles in the flexible bioenergetics required for tumor cell survival and compromising the efficacy of anti-cancer therapy. Further deciphering the cyclin B1/CDK1-controlled mitochondrial metabolism may invent effect targets to treat resistant cancers.},
}

@article {pmid30466434,
year = {2018},
author = {Petrů, M and Wideman, J and Moore, K and Alcock, F and Palmer, T and Doležal, P},
title = {Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {141},
doi = {10.1186/s12915-018-0607-3},
pmid = {30466434},
issn = {1741-7007},
support = {13-29423S//Grantová Agentura České Republiky (CZ)/ ; 1215//Grantová Agentura, Univerzita Karlova/ ; LH15253//Ministerstvo Školství, Mládeže a Tělovýchovy (CZ)/ ; LQ1604//Ministerstvo Školství, Mládeže a Tělovýchovy (CZ)/ ; CZ.1.05/1.1.00/02.0109//European Regional Development Fund ()/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//European Regional Development Fund ()/ ; },
abstract = {BACKGROUND: Bacteria and mitochondria contain translocases that function to transport proteins across or insert proteins into their inner and outer membranes. Extant mitochondria retain some bacterial-derived translocases but have lost others. While BamA and YidC were integrated into general mitochondrial protein transport pathways (as Sam50 and Oxa1), the inner membrane TAT translocase, which uniquely transports folded proteins across the membrane, was retained sporadically across the eukaryote tree.

RESULTS: We have identified mitochondrial TAT machinery in diverse eukaryotic lineages and define three different types of eukaryote-encoded TatABC-derived machineries (TatAC, TatBC and TatC-only). Here, we investigate TatAC and TatC-only machineries, which have not been studied previously. We show that mitochondria-encoded TatAC of the jakobid Andalucia godoyi represent the minimal functional pathway capable of substituting for the Escherichia coli TatABC complex and can transport at least one substrate. However, selected TatC-only machineries, from multiple eukaryotic lineages, were not capable of supporting the translocation of this substrate across the bacterial membrane. Despite the multiple losses of the TatC gene from the mitochondrial genome, the gene was never transferred to the cell nucleus. Although the major constraint preventing nuclear transfer of mitochondrial TatC is likely its high hydrophobicity, we show that in chloroplasts, such transfer of TatC was made possible due to modifications of the first transmembrane domain.

CONCLUSIONS: At its origin, mitochondria inherited three inner membrane translocases Sec, TAT and Oxa1 (YidC) from its bacterial ancestor. Our work shows for the first time that mitochondrial TAT has likely retained its unique function of transporting folded proteins at least in those few eukaryotes with TatA and TatC subunits encoded in the mitochondrial genome. However, mitochondria, in contrast to chloroplasts, abandoned the machinery multiple times in evolution. The overall lower hydrophobicity of the Oxa1 protein was likely the main reason why this translocase was nearly universally retained in mitochondrial biogenesis pathways.},
}

@article {pmid30464337,
year = {2018},
author = {Chen, YL and Chen, LJ and Chu, CC and Huang, PK and Wen, JR and Li, HM},
title = {TIC236 links the outer and inner membrane translocons of the chloroplast.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-018-0713-y},
pmid = {30464337},
issn = {1476-4687},
abstract = {The two-membrane envelope is a defining feature of chloroplasts. Chloroplasts evolved from a Gram-negative cyanobacterial endosymbiont. During evolution, genes of the endosymbiont have been transferred to the host nuclear genome. Most chloroplast proteins are synthesized in the cytosol as higher-molecular-mass preproteins with an N-terminal transit peptide. Preproteins are transported into chloroplasts by the TOC and TIC (translocons at the outer- and inner-envelope membranes of chloroplasts, respectively) machineries1,2, but how TOC and TIC are assembled together is unknown. Here we report the identification of the TIC component TIC236; TIC236 is an integral inner-membrane protein that projects a 230-kDa domain into the intermembrane space, which binds directly to the outer-membrane channel TOC75. The knockout mutation of TIC236 is embryonically lethal. In TIC236-knockdown mutants, a smaller amount of the inner-membrane channel TIC20 was associated with TOC75; the amount of TOC-TIC supercomplexes was also reduced. This resulted in a reduced import rate into the stroma, though outer-membrane protein insertion was unaffected. The size and the essential nature of TIC236 indicate that-unlike in mitochondria, in which the outer- and inner-membrane translocons exist as separate complexes and a supercomplex is only transiently assembled during preprotein translocation3,4-a long and stable protein bridge in the intermembrane space is required for protein translocation into chloroplasts. Furthermore, TIC236 and TOC75 are homologues of bacterial inner-membrane TamB5 and outer-membrane BamA, respectively. Our evolutionary analyses show that, similar to TOC75, TIC236 is preserved only in plants and has co-evolved with TOC75 throughout the plant lineage. This suggests that the backbone of the chloroplast protein-import machinery evolved from the bacterial TamB-BamA protein-secretion system.},
}

@article {pmid30443184,
year = {2018},
author = {Dou, X and Chen, L and Lei, M and Zellmer, L and Jia, Q and Ling, P and He, Y and Yang, W and Liao, DJ},
title = {Evaluating the Remote Control of Programmed Cell Death, with or without a Compensatory Cell Proliferation.},
journal = {International journal of biological sciences},
volume = {14},
number = {13},
pages = {1800-1812},
doi = {10.7150/ijbs.26962},
pmid = {30443184},
issn = {1449-2288},
abstract = {Organisms and their different component levels, whether organelle, cellular or other, come by birth and go by death, and the deaths are often balanced by new births. Evolution on the one hand has built demise program(s) in cells of organisms but on the other hand has established external controls on the program(s). For instance, evolution has established death program(s) in animal cells so that the cells can, when it is needed, commit apoptosis or senescent death (SD) in physiological situations and stress-induced cell death (SICD) in pathological situations. However, these programmed cell deaths are not predominantly regulated by the cells that do the dying but, instead, are controlled externally and remotely by the cells' superior(s), i.e. their host tissue or organ or even the animal's body. Currently, it is still unclear whether a cell has only one death program or has several programs respectively controlling SD, apoptosis and SICD. In animals, apoptosis exterminates, in a physiological manner, healthy but no-longer needed cells to avoid cell redundancy, whereas suicidal SD and SICD, like homicidal necrosis, terminate ill but useful cells, which may be followed by regeneration of the live cells and by scar formation to heal the damaged organ or tissue. Therefore, "who dies" clearly differentiates apoptosis from SD, SICD and necrosis. In animals, apoptosis can occur only in those cell types that retain a lifelong ability of proliferation and never occurs in those cell types that can no longer replicate in adulthood. In cancer cells, SICD is strengthened, apoptosis is dramatically weakened while SD has been lost. Most published studies professed to be about apoptosis are actually about SICD, which has four basic and well-articulated pathways involving caspases or involving pathological alterations in the mitochondria, endoplasmic reticula, or lysosomes.},
}

@article {pmid30421421,
year = {2018},
author = {Patten, MM},
title = {The X chromosome favors males under sexually antagonistic selection.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1111/evo.13646},
pmid = {30421421},
issn = {1558-5646},
abstract = {The X chromosome is found twice as often in females as males. This has led to an intuition that X-linked genes for traits experiencing sexually antagonistic selection should tend to evolve toward the female optimum. However, this intuition has never been formally examined. In this paper, I present a simple mathematical model and ask whether the X chromosome is indeed biased toward effecting female-optimal phenotypes. Counter to the intuition, I find that the exact opposite bias exists; the X chromosome is revealed to be a welcome spot for mutations that benefit males at the expense of females. Not only do male-beneficial alleles have an easier time of invading and spreading through a population, but they also achieve higher equilibrium frequencies than comparable female-beneficial alleles. The X chromosome is therefore expected over evolutionary time to nudge phenotypes closer to the male optimum. Consequently, the X chromosome should find itself engaged in perpetual intragenomic conflicts with the autosomes and the mitochondria over developmental outcomes. The X chromosome's male bias and the intragenomic conflicts that ensue bear on the evolution of gene regulation, speciation, and our concept of organismality.},
}

@article {pmid30419142,
year = {2018},
author = {Muthye, V and Lavrov, DV},
title = {Characterization of mitochondrial proteomes of nonbilaterian animals.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1289-1301},
doi = {10.1002/iub.1961},
pmid = {30419142},
issn = {1521-6551},
support = {//Iowa State University/ ; },
abstract = {Mitochondria require ~1,500 proteins for their maintenance and proper functionality, which constitute the mitochondrial proteome (mt-proteome). Although a few of these proteins, mostly subunits of the electron transport chain complexes, are encoded in mitochondrial DNA (mtDNA), the vast majority are encoded in the nuclear genome and imported to the organelle. Previous studies have shown a continuous and complex evolution of mt-proteome among eukaryotes. However, there was less attention paid to mt-proteome evolution within Metazoa, presumably because animal mtDNA and, by extension, animal mitochondria are often considered to be uniform. In this analysis, two bioinformatic approaches (Orthologue-detection and Mitochondrial Targeting Sequence prediction) were used to identify mt-proteins in 23 species from four nonbilaterian phyla: Cnidaria, Ctenophora, Placozoa, and Porifera, as well as two choanoflagellates, the closest animal relatives. Our results revealed a large variation in mt-proteome in nonbilaterian animals in size and composition. Myxozoans, highly reduced cnidarian parasites, possessed the smallest inferred mitochondrial proteomes, while calcareous sponges possessed the largest. About 513 mitochondrial orthologous groups were present in all nonbilaterian phyla and human. Interestingly, 42 human mitochondrial proteins were not identified in any nonbilaterian species studied and represent putative innovations along the bilaterian branch. Several of these proteins were involved in apoptosis and innate immunity, two processes known to evolve within Metazoa. Conversely, several proteins identified as mitochondrial in nonbilaterian phyla and animal outgroups were absent in human, representing cases of possible loss. Finally, a few human cytosolic proteins, such as histones and cytosolic ribosomal proteins, were predicted to be targeted to mitochondria in nonbilaterian animals. Overall, our analysis provides the first step in characterization of mt-proteomes in nonbilaterian animals and understanding evolution of animal mt-proteome. © 2018 IUBMB Life, 70(12):1289-1301, 2018.},
}

@article {pmid30417348,
year = {2018},
author = {Lasne, C and Van Heerwaarden, B and Sgrò, CM and Connallon, T},
title = {Quantifying the relative contributions of the X chromosome, autosomes, and mitochondrial genome to local adaptation.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1111/evo.13647},
pmid = {30417348},
issn = {1558-5646},
abstract = {During local adaptation with gene flow, some regions of the genome are inherently more responsive to selection than others. Recent theory predicts that X-linked genes should disproportionately contribute to local adaptation relative to other genomic regions, yet this prediction remains to be tested. We carried out a multigeneration crossing scheme, using two cline-end populations of Drosophila melanogaster, to estimate the relative contributions of the X chromosome, autosomes, and mitochondrial genome to divergence in four traits involved in local adaptation (wing size, resistance to heat, desiccation, and starvation stresses). We found that the mitochondrial genome and autosomes contributed significantly to clinal divergence in three of the four traits. In contrast, the X made no significant contribution to divergence in these traits. Given the small size of the mitochondrial genome, our results indicate that it plays a surprisingly large role in clinal adaptation. In contrast, the X, which represents roughly 20% of the Drosophila genome, contributes negligibly-a pattern that conflicts with theoretical predictions. These patterns reinforce recent work implying a central role of mitochondria in climatic adaptation, and suggest that different genomic regions may play fundamentally different roles in processes of divergence with gene flow.},
}

@article {pmid30395972,
year = {2018},
author = {Fan, PC and Zhang, Y and Wang, Y and Wei, W and Zhou, YX and Xie, Y and Wang, X and Qi, YZ and Chang, L and Jia, ZP and Zhou, Z and Guan, H and Zhang, H and Xu, P and Zhou, PK},
title = {Quantitative proteomics reveals mitochondrial respiratory chain as a dominant target for carbon ion radiation: Delayed reactive oxygen species generation caused DNA damage.},
journal = {Free radical biology & medicine},
volume = {130},
number = {},
pages = {436-445},
doi = {10.1016/j.freeradbiomed.2018.10.449},
pmid = {30395972},
issn = {1873-4596},
abstract = {Heavy ion radiotherapy has shown great promise for cancer therapy. Understanding the cellular response mechanism to heavy ion radiation is required to explore measures of overcoming devastating side effects. Here, we performed a quantitative proteomic analysis to investigate the mechanism of carbon ion irradiation on human AHH-1 lymphoblastoid cells. We identified 4602 proteins and quantified 4569 proteins showing high coverage in the mitochondria. Data are available via ProteomeXchange with identifier PXD008351. After stringent filtering, 290 proteins were found to be significantly up-regulated and 16 proteins were down-regulated. Functional analysis revealed that these up-regulated proteins were enriched in the process of DNA damage repair, mitochondrial ribosome, and particularly mitochondrial respiratory chain, accounting for approximately 50% of the accumulated proteins. Bioinformatics and functional analysis demonstrated that these up-regulated mitochondrial respiratory chain proteins enhanced ATP production and simultaneously reactive oxygen species release. More importantly, increased reactive oxygen species led to secondary organelle injury and lagged DNA double-strand breaks. Consistently, the expression of antioxidant enzymes was up-regulated for free radical scavenging. The mechanism of lagged secondary injury originated from disturbances in the mitochondrial respiratory chain. Our results provided a novel target for cell self-repair against heavy ion radiation-induced cellular damage.},
}

@article {pmid30394643,
year = {2018},
author = {Rand, DM and Mossman, JA and Zhu, L and Biancani, LM and Ge, JY},
title = {Mitonuclear epistasis, genotype-by-environment interactions, and personalized genomics of complex traits in Drosophila.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1275-1288},
doi = {10.1002/iub.1954},
pmid = {30394643},
issn = {1521-6551},
support = {NIA grant 1R01AG027849NIH grant 2R01GM067862/GF/NIH HHS/United States ; 1R01AG027849/GF/NIH HHS/United States ; 2R01GM067862/GF/NIH HHS/United States ; //Brown University/ ; },
abstract = {Mitochondrial function requires the coordinated expression of dozens of gene products from the mitochondrial genome and hundreds from the nuclear genomes. The systems that emerge from these interactions convert the food we eat and the oxygen we breathe into energy for life, while regulating a wide range of other cellular processes. These facts beg the question of whether the gene-by-gene interactions (G x G) that enable mitochondrial function are distinct from the gene-by-environment interactions (G x E) that fuel mitochondrial activity. We examine this question using a Drosophila model of mitonuclear interactions in which experimental combinations of mtDNA and nuclear chromosomes generate pairs of mitonuclear genotypes to test for epistatic interactions (G x G). These mitonuclear genotypes are then exposed to altered dietary or oxygen environments to test for G x E interactions. We use development time to assess dietary effects, and genome wide RNAseq analyses to assess hypoxic effects on transcription, which can be partitioned in to mito, nuclear, and environmental (G x G x E) contributions to these complex traits. We find that mitonuclear epistasis is universal, and that dietary and hypoxic treatments alter the epistatic interactions. We further show that the transcriptional response to alternative mitonuclear interactions has significant overlap with the transcriptional response to alternative oxygen environments. Gene coexpression analyses suggest that these shared genes are more central in networks of gene interactions, implying some functional overlap between epistasis and genotype by environment interactions. These results are discussed in the context of evolutionary fitness, the genetic basis of complex traits, and the challenge of achieving precision in personalized medicine. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1275-1288, 2018.},
}

@article {pmid30391331,
year = {2018},
author = {Xu, L and Peng, L and Gu, T and Yu, D and Yao, YG},
title = {The 3'UTR of human MAVS mRNA contains multiple regulatory elements for the control of protein expression and subcellular localization.},
journal = {Biochimica et biophysica acta. Gene regulatory mechanisms},
volume = {1862},
number = {1},
pages = {47-57},
doi = {10.1016/j.bbagrm.2018.10.017},
pmid = {30391331},
issn = {1876-4320},
abstract = {Post-transcriptional regulation controls the mRNA stability, translation efficiency, and subcellular localization of a protein. The mitochondrial antiviral signaling protein (MAVS) plays a vital role in innate antiviral immunity. The MAVS mRNA has a long 3' untranslated region (UTR, >9 kb) and an understanding of this region may help to explain the post-transcriptional regulation in a key protein. In this study, we aimed to characterize the role of the MAVS 3'UTR during MAVS expression by truncating the 3'UTR into different fragments so as to identify the regulatory elements. We found that the different fragments (H1-H5) of the MAVS 3'UTR play different roles in regulating the subcellular localization and function of MAVS. Three AU-rich elements (AREs) in the MAVS 3'UTR H1 fragment (region 1-3445 in the 3'UTR) repressed MAVS expression by interacting with HuR to destabilize its mRNA. The MAVS 3'UTR H5 fragment (region 5955-7687 in the 3'UTR) affected the cellular localization of MAVS in mitochondria and influenced the subsequent antiviral function. Four miR-27a binding sites were recognized in the MAVS 3'UTR, and treatment of miR-27a inhibited MAVS expression and promoted the replication of the vesicular stomatitis virus (VSV). The identification of multiple regulatory elements in the MAVS 3'UTR offers new insights into the precise control of MAVS expression in innate immunity.},
}

@article {pmid30390623,
year = {2018},
author = {Portugez, S and Martin, WF and Hazkani-Covo, E},
title = {Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {162},
doi = {10.1186/s12862-018-1279-x},
pmid = {30390623},
issn = {1471-2148},
support = {I-1321-203.13/2015//German-Israeli Foundation for Scientific Research and Development/ ; I-1321-203.13/2015//German-Israeli Foundation for Scientific Research and Development/ ; 666053//European Research Council/International ; },
abstract = {BACKGROUND: Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts and nupts are classified as simple if they are composed of a single organelle fragment or as complex if they are composed of multiple fragments. Mosaic insertions are complex insertions composed of fragments of both mitochondrial and plastid DNA. Simple numts and nupts in eukaryotes have been extensively studied, their mechanism of insertion involves non-homologous end joining (NHEJ). Mosaic insertions have been less well-studied and their mechanisms of integration are unknown.

RESULTS: Here we estimated the number of nuclear mosaic insertions (numins) in nine plant genomes. We show that numins compose up to 10% of the total nuclear insertions of organelle DNA in these plant genomes. The NHEJ hallmarks typical for numts and nupts were also identified in mosaic insertions. However, the number of identified insertions that integrated via NHEJ mechanism is underestimated, as NHEJ signatures are conserved only in recent insertions and mutationally eroded in older ones. A few complex insertions show signatures of long homology that cannot be attributed to NHEJ, a novel observation that implicates gene conversion or single strand annealing mechanisms in organelle nuclear insertions.

CONCLUSIONS: The common NHEJ signature that was identified here reveals that, in plant cells, mitochondria and plastid fragments in numins must meet during or prior to integration into the nuclear genome.},
}

@article {pmid30385634,
year = {2018},
author = {Loell, K and Nanda, V},
title = {Marginal protein stability drives subcellular proteome isoelectric point.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {46},
pages = {11778-11783},
doi = {10.1073/pnas.1809098115},
pmid = {30385634},
issn = {1091-6490},
support = {80NSSC18K0093//Intramural NASA/United States ; DP2 OD006478/OD/NIH HHS/United States ; },
abstract = {There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome-a highly acidic compartment in the cell-have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.},
}

@article {pmid30378025,
year = {2018},
author = {Gabaldón, T},
title = {Evolution of the Peroxisomal Proteome.},
journal = {Sub-cellular biochemistry},
volume = {89},
number = {},
pages = {221-233},
doi = {10.1007/978-981-13-2233-4_9},
pmid = {30378025},
issn = {0306-0225},
abstract = {Peroxisomes are single-membrane bound intracellular organelles that can be found in organisms across the tree of eukaryotes, and thus are likely to derive from an ancestral peroxisome in the last eukaryotic common ancestor (LECA). Yet, peroxisomes in different lineages can present a large diversity in terms of their metabolic capabilities, which reflects a highly variable proteomic content. Theories on the evolutionary origin of peroxisomes have shifted in the last decades from scenarios involving an endosymbiotic origin, similar to those of mitochondria and plastids, towards hypotheses purporting an endogenous origin from within the endomembrane system. The peroxisomal proteome is highly dynamic in evolutionary terms, and can evolve via differential loss and gain of proteins, as well as via relocalization of proteins from and to other sub-cellular compartments. Here, I review current knowledge and discussions on the diversity, origin, and evolution of the peroxisomal proteome.},
}

@article {pmid30377874,
year = {2018},
author = {Cai, C and Liu, F and Jiang, T and Wang, L and Jia, R and Zhou, L and Gu, K and Ren, J and He, P},
title = {Comparative study on mitogenomes of green tide algae.},
journal = {Genetica},
volume = {146},
number = {6},
pages = {529-540},
doi = {10.1007/s10709-018-0046-7},
pmid = {30377874},
issn = {1573-6857},
support = {18ZR1417400//Shanghai Natural Science Fund/ ; 41576163//National Natural Science Foundation of China/ ; 2016YFC1402105//National Key R&D Program of China/ ; MATHAB2017010//Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A./ ; },
abstract = {Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.},
}

@article {pmid30373839,
year = {2018},
author = {Mehta, AP and Supekova, L and Chen, JH and Pestonjamasp, K and Webster, P and Ko, Y and Henderson, SC and McDermott, G and Supek, F and Schultz, PG},
title = {Engineering yeast endosymbionts as a step toward the evolution of mitochondria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {46},
pages = {11796-11801},
doi = {10.1073/pnas.1813143115},
pmid = {30373839},
issn = {1091-6490},
support = {P41 GM103445/GM/NIGMS NIH HHS/United States ; },
abstract = {It has been hypothesized that mitochondria evolved from a bacterial ancestor that initially became established in an archaeal host cell as an endosymbiont. Here we model this first stage of mitochondrial evolution by engineering endosymbiosis between Escherichia coli and Saccharomyces cerevisiae An ADP/ATP translocase-expressing E. coli provided ATP to a respiration-deficient cox2 yeast mutant and enabled growth of a yeast-E. coli chimera on a nonfermentable carbon source. In a reciprocal fashion, yeast provided thiamin to an endosymbiotic E. coli thiamin auxotroph. Expression of several SNARE-like proteins in E. coli was also required, likely to block lysosomal degradation of intracellular bacteria. This chimeric system was stable for more than 40 doublings, and GFP-expressing E. coli endosymbionts could be observed in the yeast by fluorescence microscopy and X-ray tomography. This readily manipulated system should allow experimental delineation of host-endosymbiont adaptations that occurred during evolution of the current, highly reduced mitochondrial genome.},
}

@article {pmid30368957,
year = {2018},
author = {Olsson, M and Friesen, CR and Rollings, N and Sudyka, J and Lindsay, W and Whittingtion, CM and Wilson, M},
title = {Long term effects of superoxide and DNA repair on lizard telomeres.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.14913},
pmid = {30368957},
issn = {1365-294X},
abstract = {Telomeres are the non-coding protein-nucleotide 'caps' at chromosome ends that contribute to chromosomal stability by protecting the coding parts of the linear DNA from shortening at cell division, and from erosion by reactive molecules. Recently, there has been some controversy between molecular and cell biologists, on the one hand, and evolutionary ecologists on the other, regarding whether reactive molecules erode telomeres during oxidative stress. Many studies of biochemistry and medicine have verified these relationships in cell culture, but other researchers have failed to find such effects in free-living vertebrates. Here we use a novel approach to measure free radicals (superoxide), mitochondrial 'content' (a combined measure of mitochondrial number and size in cells), telomere length and DNA damage at two primary time points during the mating season of an annual lizard species (Ctenophorus pictus). Superoxide levels early in the mating season vary widely and elevated levels predict shorter telomeres both at that time as well as several months later. These effects are likely driven by mitochondrial content, which significantly impacts late season superoxide (cells with more mitochondria have more superoxide), but superoxide effects on telomeres are counteracted by DNA repair as revealed by 8-hydroxy-2'-deoxyguanosine assays. We conclude that reactive oxygen species and DNA repair are fundamental for both short- and long-term regulation of lizard telomere length with pronounced effects of early-season cellular stress detectable on telomere length near lizard death. This article is protected by copyright. All rights reserved.},
}

@article {pmid30358111,
year = {2018},
author = {Yu, J and Zhang, L and Li, Y and Zhu, X and Xu, S and Zhou, XM and Wang, H and Zhang, H and Liang, B and Liu, P},
title = {The Adrenal Lipid Droplet is a New Site for Steroid Hormone Metabolism.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e1800136},
doi = {10.1002/pmic.201800136},
pmid = {30358111},
issn = {1615-9861},
abstract = {Steroid hormones play essential roles for living organisms. It has been long and well established that the endoplasmic reticulum (ER) and mitochondria are essential sites for steroid hormone biosynthesis because several steroidogenic enzymes are located in these organelles. The adrenal gland lipid droplet (LD) proteomes from human, macaque monkey, and rodent were analyzed, revealing that steroidogenic enzymes are also present in abundance on LDs. The enzymes found include 3β-hydroxysteroid dehydrogenase (HSD3B), and estradiol 17β-dehydrogenase 11 (HSD17B11). Analyses by Western blot and subcellular localization consistently demonstrated that HSD3B2 was localized on LDs. Furthermore, in vitro experiments confirmed that the isolated LDs from HeLa cell stably expressing HSD3B2 or from rat adrenal glands had the capacity to convert pregnenolone to progesterone. Collectively, these data suggest that LDs may be important sites of steroid hormone metabolism. These findings may bring novel insights into the biosynthesis and metabolism of steroid hormones and the development of treatments for adrenal disorders. This article is protected by copyright. All rights reserved.},
}

@article {pmid30358065,
year = {2018},
author = {Paris, Z and Alfonzo, JD},
title = {How the intracellular partitioning of tRNA and tRNA modification enzymes affects mitochondrial function.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1207-1213},
doi = {10.1002/iub.1957},
pmid = {30358065},
issn = {1521-6551},
support = {AI131348/GF/NIH HHS/United States ; GM084065/GF/NIH HHS/United States ; CZ.02.1.01/0.0/0.0/16_019/0000759//ERDF/ESF project Centre for Research of Pathogenicity and Virulence of Parasites/ ; },
abstract = {Organisms have evolved different strategies to seclude certain molecules to specific locations of the cell. This is most pronounced in eukaryotes with their extensive intracellular membrane systems. Intracellular compartmentalization is particularly critical in genome containing organelles, which because of their bacterial evolutionary ancestry still maintain protein-synthesis machinery that resembles more their evolutionary origin than the extant eukaryotic cell they once joined as an endosymbiont. Despite this, it is clear that genome-containing organelles such as the mitochondria are not in isolation and many molecules make it across the mitochondrial membranes from the cytoplasm. In this realm the import of tRNAs and the enzymes that modify them prove most consequential. In this review, we discuss two recent examples of how modifications typically found in cytoplasmic tRNAs affect mitochondrial translation in organisms that forcibly import all their tRNAs from the cytoplasm. In our view, the combination of tRNA import and the compartmentalization of modification enzymes must have played a critical role in the evolution of the organelle. © 2018 IUBMB Life, 70(12):1207-1213, 2018.},
}

@article {pmid30358047,
year = {2018},
author = {Gabaldón, T},
title = {Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1188-1196},
doi = {10.1002/iub.1950},
pmid = {30358047},
issn = {1521-6551},
support = {ERC-2016-724173//H2020 European Research Council/ ; H2020-MSCA-ITN-2014-642095//H2020 Marie Skłodowska-Curie Actions/ ; BFU2015-67107//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; H2020-MSCA-ITN-2014-642095//Marie Sklodowska-Curie/ ; ERC-2016-724173//European Union's Horizon 2020/ ; SGR857//Catalan Research Agency/ ; //CERCA Programme/Generalitat de Catalunya/ ; //European Regional Development Fund/ ; BFU2015-67107//Spanish Ministry of Economy, Industry, and Competitiveness/ ; SEV-2012-0208//Spanish Ministry of Economy, Industry, and Competitiveness/ ; },
abstract = {The origin of eukaryotes stands as a major open question in biology. Central to this question is the nature and timing of the origin of the mitochondrion, an ubiquitous eukaryotic organelle originated by the endosymbiosis of an alphaproteobacterial ancestor. Different hypotheses disagree, among other aspects, on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host is debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Here, I will discuss recent findings from phylogenomics analyses of extant genomes that are shedding light into the evolutionary origins of the eukaryotic ancestor, and which suggest a later acquisition of alpha-proteobacterial derived proteins as compared to those with different bacterial ancestries. I argue that simple eukaryogenesis models that assume a binary symbiosis between an archaeon host and an alpha-proteobacterial proto-mitochondrion cannot explain the complex chimeric nature that is inferred for the eukaryotic ancestor. To reconcile existing hypotheses with the new data, I propose the "pre-mitochondrial symbioses" hypothesis that provides a framework for eukaryogenesis scenarios involving alternative symbiotic interactions that predate the acquisition of mitochondria. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1188-1196, 2018.},
}

@article {pmid30347487,
year = {2018},
author = {Ligas, J and Pineau, E and Bock, R and Huynen, MA and Meyer, EH},
title = {The assembly pathway of complex I in Arabidopsis thaliana.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.14133},
pmid = {30347487},
issn = {1365-313X},
support = {//Centre National pour la Recherche Scientifique/ ; //Max Planck Society/ ; PIRG256398//Marie Curie International Reintegration Grant/ ; },
abstract = {All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor more than a billion years ago. However, to date, many aspects of mitochondrial evolution have remained unresolved. Comparative genomics and proteomics have revealed a complex evolutionary origin for many mitochondrial components. To understand the evolution of the respiratory chain, we have examined both the components and the mechanisms of the assembly pathway of complex I. Complex I represents the first enzyme in the respiratory chain, and complex I deficiencies have dramatic consequences in both animals and plants. The complex is located in the mitochondrial inner membrane and possesses two arms: one embedded in the inner membrane and one protruding in the matrix. Here, we describe the assembly pathway of complex I in the model plant Arabidopsis thaliana. Using a proteomics approach called complexome profiling, we have resolved the different steps in the assembly process in plants. We propose a model for the stepwise assembly of complex I, including every subunit. We then compare this pathway with the corresponding pathway in humans and find that complex I assembly in plants follows a different, and likely ancestral, pathway compared with the one in humans. We show that the main evolutionary changes in complex I structure and assembly in humans occurred at the level of the membrane arm, whereas the matrix arm remained rather conserved.},
}

@article {pmid30341492,
year = {2018},
author = {Arakawa, T and Ue, S and Sano, C and Matsunaga, M and Kagami, H and Yoshida, Y and Kuroda, Y and Taguchi, K and Kitazaki, K and Kubo, T},
title = {Identification and characterization of a semi-dominant restorer-of-fertility 1 allele in sugar beet (Beta vulgaris).},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00122-018-3211-6},
pmid = {30341492},
issn = {1432-2242},
support = {18K05564//Japan Society for the Promotion of Science/ ; 16J01146//Japan Society for the Promotion of Science/ ; Research program on development of innovative technology//Bio-oriented Technology Research Advancement Institution/ ; Grant Number 30001A//Bio-oriented Technology Research Advancement Institution/ ; },
abstract = {KEY MESSAGE: The sugar beet Rf1 locus has a number of molecular variants. We found that one of the molecular variants is a weak allele of a previously identified allele. Male sterility (MS) caused by nuclear-mitochondrial interaction is called cytoplasmic male sterility (CMS) in which MS-inducing mitochondria are suppressed by a nuclear gene, restorer-of-fertility. Rf and rf are the suppressing and non-suppressing alleles, respectively. This dichotomic view, however, seems somewhat unsatisfactory to explain the recently discovered molecular diversity of Rf loci. In the present study, we first identified sugar beet line NK-305 as a new source of Rf1. Our crossing experiment revealed that NK-305 Rf1 is likely a semi-dominant allele that restores partial fertility when heterozygous but full fertility when homozygous, whereas Rf1 from another sugar beet line appeared to be a dominant allele. Proper degeneration of anther tapetum is a prerequisite for pollen development; thus, we compared tapetal degeneration in the NK-305 Rf1 heterozygote and the homozygote. Degeneration occurred in both genotypes but to a lesser extent in the heterozygote, suggesting an association between NK-305 Rf1 dose and incompleteness of tapetal degeneration leading to partial fertility. Our protein analyses revealed a quantitative correlation between NK-305 Rf1 dose and a reduction in the accumulation of a 250 kDa mitochondrial protein complex consisting of a CMS-specific mitochondrial protein encoded by MS-inducing mitochondria. The abundance of Rf1 transcripts correlated with NK-305 Rf1 dose. The molecular organization of NK-305 Rf1 suggested that this allele evolved through intergenic recombination. We propose that the sugar beet Rf1 locus has a series of multiple alleles that differ in their ability to restore fertility and are reflective of the complexity of Rf evolution.},
}

@article {pmid30333973,
year = {2018},
author = {Lou, E and Zhai, E and Sarkari, A and Desir, S and Wong, P and Iizuka, Y and Yang, J and Subramanian, S and McCarthy, J and Bazzaro, M and Steer, CJ},
title = {Cellular and Molecular Networking Within the Ecosystem of Cancer Cell Communication via Tunneling Nanotubes.},
journal = {Frontiers in cell and developmental biology},
volume = {6},
number = {},
pages = {95},
doi = {10.3389/fcell.2018.00095},
pmid = {30333973},
issn = {2296-634X},
abstract = {Intercellular communication is vital to the ecosystem of cancer cell organization and invasion. Identification of key cellular cargo and their varied modes of transport are important considerations in understanding the basic mechanisms of cancer cell growth. Gap junctions, exosomes, and apoptotic bodies play key roles as physical modalities in mediating intercellular transport. Tunneling nanotubes (TNTs)-narrow actin-based cytoplasmic extensions-are unique structures that facilitate direct, long distance cell-to-cell transport of cargo, including microRNAs, mitochondria, and a variety of other sub cellular components. The transport of cargo via TNTs occurs between malignant and stromal cells and can lead to changes in gene regulation that propagate the cancer phenotype. More notably, the transfer of these varied molecules almost invariably plays a critical role in the communication between cancer cells themselves in an effort to resist death by chemotherapy and promote the growth and metastases of the primary oncogenic cell. The more traditional definition of "Systems Biology" is the computational and mathematical modeling of complex biological systems. The concept, however, is now used more widely in biology for a variety of contexts, including interdisciplinary fields of study that focus on complex interactions within biological systems and how these interactions give rise to the function and behavior of such systems. In fact, it is imperative to understand and reconstruct components in their native context rather than examining them separately. The long-term objective of evaluating cancer ecosystems in their proper context is to better diagnose, classify, and more accurately predict the outcome of cancer treatment. Communication is essential for the advancement and evolution of the tumor ecosystem. This interplay results in cancer progression. As key mediators of intercellular communication within the tumor ecosystem, TNTs are the central topic of this article.},
}

@article {pmid30326913,
year = {2018},
author = {Zhu, Y and Gu, X and Xu, C},
title = {Mitochondrial DNA 7908-8816 region mutations in maternally inherited essential hypertensive subjects in China.},
journal = {BMC medical genomics},
volume = {11},
number = {1},
pages = {89},
doi = {10.1186/s12920-018-0408-0},
pmid = {30326913},
issn = {1755-8794},
support = {BL2013022//special fund for clinical medicine of Jiangsu province/ ; JS2006038//Health Department of Jiangsu Province (CN)/ ; },
abstract = {BACKGROUND: Nuclear genes or family-based mitochondrial screening have been the focus of genetic studies into essential hypertension. Studies into the role of mitochondria in sporadic Chinese hypertensives are lacking. The objective of the study was to explore the relationship between mitochondrial DNA (mtDNA) variations and the development of maternally inherited essential hypertension (MIEH) in China.

METHODS: Yangzhou residents who were outpatients or in-patients at the Department of Cardiology in Northern Jiangsu People's Hospital (Jiangsu, China) from June 2009 to June 2015 were recruited in a 1:1 case control study of 600 gender-matched Chinese MIEH subjects and controls. Genomic DNA was isolated from whole blood cells. The most likely sites for hypertension were screened using oligodeoxynucleotides at positions 7908-8816, purified and subsequently analyzed by direct sequencing according to the revised consensus Cambridge sequence. The frequency, density, type and conservative evolution of mtDNA variations were comprehensively analyzed.

RESULTS: We found a statistical difference between the two groups for body mass index, waist circumference, abdominal circumference, triglyceride, low-density lipoprotein cholesterol, fasting blood glucose, uric acid, creatinine and blood urea nitrogen (P < 0.05). More amino-acid changes and RNA variants were found in MIEH subjects than the controls (P < 0.01). The detection system simultaneously identified 40 different heteroplasmic or homoplasmic mutations in 4 genes: COXII, tRNALys, ATP8 and ATP 6. The mtDNA variations were mainly distributed in regions of ATP6 binding sites, and the site of highest mutation frequency was m. 8414C > T. Three changes in single bases (C8414T in ATP8, A8701G in ATP6 and G8584A in ATP6) were significantly different in the MIEH patients and the controls (P < 0.001). The m.8273_8281del mutation was identified from 59 MIEH patients.

CONCLUSIONS: Our results indicate that novel mtDNA mutations may be involved in the pathological process of MIEH, and mitochondrial genetic characteristics were identified in MIEH individuals.},
}

@article {pmid30316921,
year = {2019},
author = {Gao, XM and Mu, DL and Hou, CC and Zhu, JQ and Jin, S and Wang, CL},
title = {Expression and putative functions of KIFC1 for nuclear reshaping and midpiece formation during spermiogenesis of Phascolosoma esculenta.},
journal = {Gene},
volume = {683},
number = {},
pages = {169-183},
doi = {10.1016/j.gene.2018.10.021},
pmid = {30316921},
issn = {1879-0038},
mesh = {Animals ; Binding Sites ; Cell Nucleus/metabolism ; Gene Expression Regulation ; Kinesin/chemistry/*genetics/*metabolism ; Male ; Microtubules/metabolism ; Models, Molecular ; Phylogeny ; Polychaeta/genetics/*physiology ; Protein Conformation ; Protein Domains ; Protein Transport ; *Spermatogenesis ; },
abstract = {Kinesin-14 KIFC1 plays an important role in vesicular transport, microtubule organization, and spermiogenesis. In this study, we first investigated the microtubule distribution and expression pattern of KIFC1 during spermiogenesis of P. esculenta. Microtubules are abundant during spermiogenesis of P. esculenta and may be related to the generation and maintenance of pseudopodia-like cytoplasmic protrusions and nuclear reshaping. The Pe-KIFC1 protein is conserved with a motor domain where microtubule and ATP binding sites are predicted, a coiled-coil domain and a divergent tail domain. The Pe-kifc1 gene was extensively expressed and showed the highest expression in coelomic fluid where spermiogenesis occurs. We further observed the expression of kifc1 mRNA and protein and found that Pe-KIFC1 protein primarily co-localized with microtubules during spermiogenesis, indicating that KIFC1 might play several roles during this process via its cargo transport and/or microtubule organization function. In addition, co-localization of mitochondria and KIFC1 was also detected during spermiogenesis, which were located in the midpiece in mature sperm, suggesting that mitochondria might be a cargo of Pe-KIFC1 that participates in the intracellular distribution of mitochondria and formation of the midpiece. Based on our detailed observations of the dynamic distribution of microtubules, KIFC1, and mitochondria during spermiogenesis and the conserved function of KIFC1 in cargo transport and microtubule organization, functional models of Pe-KIFC1 during spermiogenesis are proposed, including the participation of KIFC1 in nuclear reshaping and midpiece formation.},
}

Animals
Binding Sites
Cell Nucleus/metabolism
Gene Expression Regulation
Kinesin/chemistry/*genetics/*metabolism
Male
Microtubules/metabolism
Models, Molecular
Phylogeny
Polychaeta/genetics/*physiology
Protein Conformation
Protein Domains
Protein Transport
*Spermatogenesis

@article {pmid30304578,
year = {2018},
author = {Burger, G and Valach, M},
title = {Perfection of eccentricity: Mitochondrial genomes of diplonemids.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1197-1206},
doi = {10.1002/iub.1927},
pmid = {30304578},
issn = {1521-6551},
support = {MOP-79309//Canadian Institutes of Health Research/Canada ; GBMF-4983//Gordon and Betty Moore Foundation/ ; RGPIN-2014-05286//NSERC/ ; },
abstract = {Mitochondria are the sandbox of evolution as exemplified most particularly by the diplonemids, a group of marine microeukaryotes. These protists are uniquely characterized by their highly multipartite mitochondrial genome and systematically fragmented genes whose pieces are spread out over several dozens of chromosomes. The type species Diplonema papillatum was the first member of this group in which the expression of fragmented mitochondrial genes was investigated experimentally. We now know that gene expression involves separate transcription of gene pieces (modules), RNA editing of module transcripts, and module joining to mature mRNAs and rRNAs. The mechanism of cognate module recognition and ligation is distinct from known intron splicing and remains to be uncovered. Here, we review the current status of research on mitochondrial genome architecture, as well as gene complement, structure, and expression modes in diplonemids. Further, we discuss the potential molecular mechanisms of posttranscriptional processing, and finally reflect on the evolutionary trajectories and trends of mtDNA evolution as seen in this protist group. © 2018 IUBMB Life, 70(12):1197-1206, 2018.},
}

@article {pmid30304531,
year = {2018},
author = {Urantowka, AD and Kroczak, A and Silva, T and Padrón, RZ and Gallardo, NF and Blanch, J and Blanch, B and Mackiewicz, P},
title = {New insight into parrots' mitogenomes indicates that their ancestor contained a duplicated region.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msy189},
pmid = {30304531},
issn = {1537-1719},
abstract = {Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate PCR strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.},
}

@article {pmid30281911,
year = {2018},
author = {van Esveld, SL and Huynen, MA},
title = {Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1240-1250},
doi = {10.1002/iub.1940},
pmid = {30281911},
issn = {1521-6551},
support = {//Radboud Institute for Molecular Life Sciences/ ; R0002792//Radboudumc/ ; },
abstract = {Most eukaryotic cells contain mitochondria with a genome that evolved from their α-proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins. In this review, we examine mitochondrial gene expression from an evolutionary point of view: to what extent can we correlate changes in the mitochondrial genome in the evolutionary lineage leading to human with the origin of new nuclear encoded proteins. We dated the evolutionary origin of mitochondrial proteins that interact with mitochondrial DNA or its RNA and/or protein products in a systematic manner and compared them with documented changes in the mitochondrial DNA. We find anecdotal but accumulating evidence that metazoan RNA-interacting proteins arose in conjunction with changes of the mitochondrial DNA. We find no substantial evidence for such compensatory evolution in new OXPHOS proteins, which appear to be constrained by the ability to form supercomplexes. © 2018 IUBMB Life, 70(12):1240-1250, 2018.},
}

@article {pmid30281880,
year = {2018},
author = {Harborne, SPD and Kunji, ERS},
title = {Calcium-regulated mitochondrial ATP-Mg/Pi carriers evolved from a fusion of an EF-hand regulatory domain with a mitochondrial ADP/ATP carrier-like domain.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1222-1232},
doi = {10.1002/iub.1931},
pmid = {30281880},
issn = {1521-6551},
support = {MC_UU_00015/1//Medical Research Council/United Kingdom ; },
abstract = {The mitochondrial ATP-Mg/Pi carrier is responsible for the calcium-dependent regulation of adenosine nucleotide concentrations in the mitochondrial matrix, which allows mitochondria to respond to changing energy requirements of the cell. The carrier is expressed in mitochondria of fungi, plants and animals and belongs to the family of mitochondrial carriers. The carrier is unusual as it consists of three separate domains: (i) an N-terminal regulatory domain with four calcium-binding EF-hands similar to calmodulin, (ii) a loop domain containing an amphipathic α-helix and (iii) a mitochondrial carrier domain related to the mitochondrial ADP/ATP carrier. This striking example of three domains coming together from different origins to provide new functions represents an interesting quirk of evolution. In this review, we outline how the carrier was identified and how its physiological role was established with a focus on human isoforms. We exploit the sequence and structural information of the domains to explore the similarities and differences to their closest counterparts; mitochondrial ADP/ATP carriers and proteins with four EF-hands. We discuss how their combined function has led to a mechanism for calcium-regulated transport of adenosine nucleotides. Finally, we compare the ATP-Mg/Pi carrier with the mitochondrial aspartate/glutamate carrier, the only other mitochondrial carrier regulated by calcium, and we will argue that they have arisen by convergent rather than divergent evolution. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1222-1232, 2018.},
}

@article {pmid30265295,
year = {2018},
author = {Pereira, J and Lupas, AN},
title = {The Origin of Mitochondria-Specific Outer Membrane β-Barrels from an Ancestral Bacterial Fragment.},
journal = {Genome biology and evolution},
volume = {10},
number = {10},
pages = {2759-2765},
doi = {10.1093/gbe/evy216},
pmid = {30265295},
issn = {1759-6653},
abstract = {Outer membrane β-barrels (OMBBs) are toroidal arrays of antiparallel β-strands that span the outer membrane of Gram-negative bacteria and eukaryotic organelles. Although homologous, most families of bacterial OMBBs evolved through the independent amplification of an ancestral ββ-hairpin. In mitochondria, one family (SAM50) has a clear bacterial ancestry; the origin of the other family, consisting of 19-stranded OMBBs found only in mitochondria (MOMBBs), is substantially unclear. In a large-scale comparison of mitochondrial and bacterial OMBBs, we find evidence that the common ancestor of all MOMBBs emerged by the amplification of a double ββ-hairpin of bacterial origin, probably at the time of the Last Eukaryotic Common Ancestor. Thus, MOMBBs are indeed descended from bacterial OMBBs, but their fold formed independently in the proto-mitochondria, possibly in response to the need for a general-purpose polypeptide importer. This occurred by a process of amplification, despite the final fold having a prime number of strands.},
}

@article {pmid30258733,
year = {2018},
author = {Huang, Y and Zheng, S and Mei, X and Yu, B and Sun, B and Li, B and Wei, J and Chen, J and Li, T and Pan, G and Zhou, Z and Li, C},
title = {A secretory hexokinase plays an active role in the proliferation of Nosema bombycis.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5658},
doi = {10.7717/peerj.5658},
pmid = {30258733},
issn = {2167-8359},
abstract = {The microsporidian Nosema bombycis is an obligate intracellular parasite of Bombyx mori, that lost its intact tricarboxylic acid cycle and mitochondria during evolution but retained its intact glycolysis pathway. N. bombycis hexokinase (NbHK) is not only a rate-limiting enzyme of glycolysis but also a secretory protein. Indirect immunofluorescence assays and recombinant HK overexpressed in BmN cells showed that NbHK localized in the nucleus and cytoplasm of host cell during the meront stage. When N. bombycis matured, NbHK tended to concentrate at the nuclei of host cells. Furthermore, the transcriptional profile of NbHK implied it functioned during N. bombycis' proliferation stages. A knock-down of NbHK effectively suppressed the proliferation of N. bombycis indicating that NbHK is an important protein for parasite to control its host.},
}

@article {pmid30256727,
year = {2018},
author = {McClelland, GB and Scott, GR},
title = {Evolved Mechanisms of Aerobic Performance and Hypoxia Resistance in High-Altitude Natives.},
journal = {Annual review of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-physiol-021317-121527},
pmid = {30256727},
issn = {1545-1585},
abstract = {Comparative physiology studies of high-altitude species provide an exceptional opportunity to understand naturally evolved mechanisms of hypoxia resistance. Aerobic capacity (VO2max) is a critical performance trait under positive selection in some high-altitude taxa, and several high-altitude natives have evolved to resist the depressive effects of hypoxia on VO2max. This is associated with enhanced flux capacity through the O2 transport cascade and attenuation of the maladaptive responses to chronic hypoxia that can impair O2 transport. Some highlanders exhibit elevated rates of carbohydrate oxidation during exercise, taking advantage of its high ATP yield per mole of O2. Certain highland native animals have also evolved more oxidative muscles and can sustain high rates of lipid oxidation to support thermogenesis. The underlying mechanisms include regulatory adjustments of metabolic pathways and to gene expression networks. Therefore, the evolution of hypoxia resistance in high-altitude natives involves integrated functional changes in the pathways for O2 and substrate delivery and utilization by mitochondria. Expected final online publication date for the Annual Review of Physiology Volume 81 is February 10, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid30246391,
year = {2018},
author = {Shibata, D},
title = {Somatic cell evolution: how to improve with age.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.5173},
pmid = {30246391},
issn = {1096-9896},
support = {U54CA217376//National Institutes of Health/ ; CA196569//National Institutes of Health/ ; P30CA014089//National Institutes of Health/ ; },
abstract = {A recent article published in this journal illuminates a rare example of somatic evolution where cells improve rather than deteriorate with age. In mitotic intestinal crypts, stem cells with higher levels of a deleterious heteroplasmic germline mitochondrial mutation are purged through time, leading to crypts without the mutation. Similar somatic mitochondrial mutations are not purged from crypts, indicating that special conditions are needed to improve with age. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.},
}

@article {pmid30211573,
year = {2018},
author = {Geary, DC},
title = {Efficiency of mitochondrial functioning as the fundamental biological mechanism of general intelligence (g).},
journal = {Psychological review},
volume = {125},
number = {6},
pages = {1028-1050},
doi = {10.1037/rev0000124},
pmid = {30211573},
issn = {1939-1471},
abstract = {General intelligence or g is one of the most thoroughly studied concepts in the behavioral sciences. Measures of intelligence are predictive of a wide range of educational, occupational, and life outcomes, including creative productivity and are systematically related to physical health and successful aging. The nexus of relations suggests 1 or several fundamental biological mechanisms underlie g, health, and aging, among other outcomes. Cell-damaging oxidative stress has been proposed as 1 of many potential mechanisms, but the proposal is underdeveloped and does not capture other important mitochondrial functions. I flesh out this proposal and argue that the overall efficiency of mitochondrial functioning is a core component of g; the most fundamental biological mechanism common to all brain and cognitive processes and that contributes to the relations among intelligence, health, and aging. The proposal integrates research on intelligence with models of the centrality of mitochondria to brain development and functioning, neurological diseases, and health more generally. Moreover, the combination of the maternal inheritance of mitochondrial DNA (mtDNA), the evolution of compensatory nuclear DNA, and the inability of evolutionary processes to purge deleterious mtDNA in males may contribute to the sex difference in variability in intelligence and in other cognitive domains. The proposal unifies many now disparate literatures and generates testable predictions for future studies. (PsycINFO Database Record (c) 2018 APA, all rights reserved).},
}

@article {pmid30209549,
year = {2018},
author = {Sandor, S and Zhang, Y and Xu, J},
title = {Fungal mitochondrial genomes and genetic polymorphisms.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9350-5},
pmid = {30209549},
issn = {1432-0614},
support = {531998//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Mitochondria are the powerhouses of eukaryotic cells, responsible for ATP generation and playing a role in a diversity of cellular and organismal functions. Different from the majority of other intracellular membrane structures, mitochondria contain their own genetic materials that are capable of independent replication and inheritance. In this mini-review, we provide brief summaries of fungal mitochondrial genome structure, size, gene content, inheritance, and genetic variation. We pay special attention to the relative genetic polymorphisms of the mitochondrial vs nuclear genomes at the population level within individual fungal species. Among the 20 species/groups of species reviewed here, there is a range of variation among genes and species in the relative nuclear and mitochondrial genetic polymorphisms. Interestingly, most (15/20) showed a greater genetic diversity for nuclear genes and genomes than for mitochondrial genes and genomes, with the remaining five showing similar or slower nuclear genome genetic variations. This fungal pattern is different from the dominant pattern in animals, but more similar to that in plants. At present, the mechanisms for the variations among fungal species and the overall low level of mitochondrial sequence polymorphisms are not known. The increasing availability of population genomic data should help us reveal the potential genetic and ecological factors responsible for the observed variations.},
}

@article {pmid30206380,
year = {2018},
author = {Jebb, D and Foley, NM and Whelan, CV and Touzalin, F and Puechmaille, SJ and Teeling, EC},
title = {Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13634},
doi = {10.1038/s41598-018-31093-2},
pmid = {30206380},
issn = {2045-2322},
support = {ERC-2012-StG311000//EC | European Research Council (ERC)/ ; },
abstract = {Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The "Free Radical Theory of Ageing" (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.},
}

@article {pmid30196672,
year = {2018},
author = {Eom, KS and Park, H and Lee, D and Choe, S and Kang, Y and Bia, MM and Lee, SH and Keyyu, J and Fyumagwa, R and Jeon, HK},
title = {Molecular and Morphologic Identification of Spirometra ranarum Found in the Stool of African Lion, Panthera leo in the Serengeti Plain of Tanzania.},
journal = {The Korean journal of parasitology},
volume = {56},
number = {4},
pages = {379-383},
doi = {10.3347/kjp.2018.56.4.379},
pmid = {30196672},
issn = {1738-0006},
support = {2017R1D1A3B03035976//National Research Foundation of Korea/ ; PRB000720//Parasite Resource Bank of Korea/ ; },
mesh = {Animals ; Cyclooxygenase 1/genetics ; Feces/*parasitology ; Host-Parasite Interactions ; Lions/*parasitology ; Male ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Spirometra/anatomy & histology/*genetics/*isolation & purification ; Tanzania ; },
abstract = {The present study was performed with morphological and molecular analysis (cox1 and nad1 mitochondrial genes) to identify the proglottids of spirometrid tapeworm found in the stool of an African lion, Panthera leo, in the Serengeti plain of Tanzania. A strand of tapeworm strobila, about 75 cm in length, was obtained in the stool of a male African lion in the Serengeti National Park (34˚ 50' E, 02˚ 30' S), Tanzania, in February 2012. The morphological features of the adult worm examined exhibited 3 uterine coils with a bow tie appearance and adopted a diagonal direction in the second turn. The posterior uterine coils are larger than terminal uterine ball and the feature of uteri are swirling rather than spirally coiling. The sequence difference between the Spirometra species (Tanzania origin) and S. erinaceieuropaei (GenBank no. KJ599680) was 9.4% while those of S. decipiens (GenBank no. KJ599679) differed by 2.1% in the cox1 and nad1 genes. Phylogenetic tree topologies generated using the 2 analytic methods were identical and presented high level of confidence values for the 3 major branches of the 3 Spirometra species in the cox1 gene. The morphological and molecular findings obtained in this study were nearly coincided with those of S. ranarum. Therefore, we can know for the first time that the African lion, Panthera leo, is to the definitive host of this tapeworm.},
}

Animals
Cyclooxygenase 1/genetics
Feces/*parasitology
Host-Parasite Interactions
Lions/*parasitology
Male
Mitochondria/genetics
NADH Dehydrogenase/genetics
Phylogeny
Spirometra/anatomy & histology/*genetics/*isolation & purification
Tanzania