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410 results for “Mitochondrial gene”
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
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Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
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Temporal dynamics of mildly deleterious nonsynonymous substitutions in mitochondrial gene sequences in rodents and moles
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Mitochondrial genes have incongruent histories linked to their chromosomal position and function
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Data for: Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome
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Data from: Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird
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Data from: Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?
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Complex histories of gene flow and a mitochondrial capture event in a non-sister pair of bird
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Data from: Ancient mitochondrial gene transfer between fungi and the orchids
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Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)
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Data from: The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents
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Mitochondrial genes from eighteen angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants
<p class="Default"><span>The early diversification of angiosperms is a rapid yet complicated process and thus it renders the phylogenetic analyses of early-diverging angiosperms much difficulty. Plastid and nuclear phylogenomic studies have raised several controversial hypotheses regarding the angiosperm phylogeny, whereas mitochondrial genomes have been largely ignored. In this study, we newly sequenced mitochondrial genomes from 18 angiosperms to fill the sampling gaps in magnoliids, Austrobaileyales, Chloranthales, Ceratophyllales, and early-diverging lineages of eudicots and monocots. A data matrix of 38 mitochondrial genes from 107 taxa was assembled to address this question. Although conflicting phylogenies were recovered in this study from different datasets and analytical methods, congruence was achieved regarding the deep relationships of several major angiosperm lineages: Chloranthales always groups with Ceratophyllales, Austrobaileyales is sister to mesangiosperms, and a previously unplaced clade—Dilleniales—is consistently resolved as a sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are suggested as common reasons for the noisy signals that impact phylogenetic reconstructions, and angiosperm mitochondrial genes seem to hardly suffer from these factors. In addition, the 3<sup>rd</sup> codon positions of the mitochondrial genes contained more phylogenetic signals than the 1<sup>st</sup> and 2<sup>nd</sup> codon positions, which might be responsible for the incongruent results recovered among different datasets. Due to the rapid radiation process, the relationships among these early lineages are not well resolved. Nevertheless, this study based on mitochondrial genomes provides additional evidence and alternative hypotheses for the early evolution and diversification of angiosperms.</span></p>
Data from: Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda)
Helicoidea is a diverse group of globally distributed land snails. While much is known regardingthe relationships of helicoid taxa, comparatively little is known about the evolution of themitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomesfrom Praticolella mexicana Perez, 2011 representing the first such data from the helicoid familyPolygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We foundthe mitochondrial genome of P. mexicana to be 14,008 bp in size, possessing the typical 37metazoan genes. Multiple alternate stop codons are used, as are incomplete stop codons, andmitogenome size and nucleotide content is consistent with other helicoid species. Our analysis ofgene order suggested that Helicoidea has undergone five mitochondrial rearrangements in thepast. Four rearrangements were limited to tRNA genes, including one homoplasticrearrangement in Helicidae and (Bradybaenidae+Camaena+P. mexicana). The fifthrearrangement, unique to Aegista, involved a protein coding gene.
Data from: Phylogeny of Anophelinae using mitochondrial protein coding genes
Malaria is a vector-borne disease that is a great burden on the poorest and most marginalized communities of the tropical and subtropical world. About 41 species of Anopheline mosquitoes can effectively spread species of Plasmodium parasites that cause human malaria. Proposing a natural classification for the subfamily Anophelinae has been a continuous effort, addressed using both morphology and DNA sequence data. Monophyly of the genus Anopheles, and phylogenetic placement of the genus Bironella, subgenera Kerteszia, Lophopodomyia, and Stethomyia within the subfamily Anophelinae, remain in question. To understand the classification of Anophelinae we inferred the phylogeny of all three genera (Anopheles, Bironella, Chagasia) and major subgenera by analyzing the amino acid sequences of the 13 protein coding genes of 150 newly sequenced mitochondrial genomes of Anophelinae and 18 newly sequenced Culex species as outgroup taxa, supplemented with 23 mitogenomes from GenBank. Our analyses generally place genus Bironella within the genus Anopheles, which implies that the latter as it is currently defined is not monophyletic. With some inconsistencies, Bironella was placed within the major clade that includes Anopheles, Cellia, Kerteszia, Lophopodomyia, Nyssorhynchus, and Stethomyia, which were found to be monophyletic groups within Anophelinae. Our findings provided robust evidence for elevating the monophyletic groupings Kerteszia, Lophopodomyia, Nyssorhynchus, and Stethomyia to genus level; genus Anopheles to include subgenera Anopheles, Baimaia, Cellia and Christya; Anopheles parvus to be placed into a new genus; Nyssorhynchus to be elevated to genus level; the genus Nyssorhynchus to include subgenera Myzorhynchella and Nyssorhynchus; Anopheles atacamensis and Anopheles pictipennis to be transferred from subgenus Nyssorhynchus to subgenus Myzorhynchella; and subgenus Nyssorhynchus to encompass the remaining species of Argyritarsis and Albimanus Sections.
Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study, next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina HiSeq 2500 instrument. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
Data from: Elevated genetic diversity of mitochondrial genes in asexual populations of bark lice ("Psocoptera": Echmepteryx hageni)
Asexual reproduction is commonly thought to be associated with low genetic diversity in animals. Echmepteryx hageni (Insecta: "Psocoptera") is one of several psocopteran species that are primarily parthenogenetic, but also exists in small, isolated sexual populations. We used mitochondrial DNA sequences to investigate the population history and genealogical relationships between the sexual and asexual forms of this species. The asexual population of E. hageni exhibits extremely high mitochondrial haplotype diversity (H = 0.98), whereas the sexual forms had significantly lower haplotypic diversity (H = 0.25, after correcting for sample size). This diversity in asexuals represents one the greatest genetic diversities reported for asexual animals in the literature. Nucleotide diversities were also higher in asexual compared to sexual populations (π = 0.0071 vs. 0.00027). Compared to other reported estimates of π in insects, asexual nucleotide diversity is high, but not remarkably elevated. Three hypotheses might explain the elevated genetic diversity of asexual populations: 1) larger effective population size, 2) greater mutation rate, or 3) possible recent origin of sexuals. In addition, phylogeographic analysis revealed little geographic structure among asexual E. hageni, although specimens from the upper Midwest form a single clade and are genetically differentiated. The mismatch distribution and neutrality tests indicate a historical population size increase, possibly associated with expansion from glacial refugia.
Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness
We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available data sets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.
Figure 1 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852
Figure 1 - Mitochondrial genome sequenced in the present study. Gene order and sizes are shown relative to one another, including non-coding regions. Protein-coding genes encoded on the light strand are underlined. Transfer RNA (tRNA) genes encoded on the light strand are underlined. Each tRNA gene is designated by a single-letter amino acid code, except L1 (trnLeu (CUN)), L2 (trnLeu (UUR)), S1 (trnSer (AGN)) and S2 (trnSer (UCN)). Numbers inside circles represent the size of the non-coding region separating two adjacent genes or the amount of shared nucleotides between two overlapping genes. The translocations of gene or gene block are shaded gray.
Figure 2 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852
Figure 2 - Phylogenetic analyses derived for brachyurans using the maximum likelihood (ML) analyses and Bayesian inferences (BI) using dataset A (13 PCGs) and dataset B (13 PCGs + two rRNAs). Branch lengths and topologies came from ML analysis. Values at the branches represent BP (Bootstrap value)/BPP (Bayesian posterior probability). 100/1.00 is denoted by an asterisk. The horizontal line stands for BP under 50 or BPP under 0.9 ML analyses. The gene rearrangement is denoted by the block on (A): (I) the translocation of trnH shared by the Brachyura taxa sampled; (II) the transposition of trnQ shared by potamid species; (III) the five-gene block, (trnM-nad2-trnW-trnC-trnY), translocation shared by three Sinopotamon crabs sampled.
data and code for Identification of mitochondrial energy metabolism genes associated with OSAS
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Allen Brain Atlas
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