Mitochondrial Genome Structure Research Articles

Mitochondrial genomes – unity and diversity

The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene transfers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.

The complete mitochondrial genome of Aeschrocoristuberculatus and A.ceylonicus (Hemiptera, Pentatomidae) and its phylogenetic implications.

Aeschrocoristuberculatus and A.ceylonicus (Hemiptera, Pentatomidae, Pentatominae) are mainly distributed in southern China, India, Myanmar, and Sri Lanka. Both species are also common agricultural pests. However, only the morphology of the genus Aeschrocoris has previously been studied, and molecular data have been lacking. In this study, the whole mitochondrial genomes of A.tuberculatus and A.ceylonicus are and annotated. The lengths of the complete mitochondrial genomes of the two species are 16,134 bp and 16,142 bp, respectively, and both contain 37 typical genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region. The mitochondrial genome structure, gene order, nucleotide composition, and codon usage of A.tuberculatus and A.ceylonicus are consistent with those of typical Pentatomidae. Most PCGs of both species use ATN as the start codon, except atp8, nad1, and cox1, which use TTG as the start codon. cox1, cox2, and atp6 use a single T, and nad1 use TAG as the stop codon; the remaining PCGs have TAA as the stop codon. The A+T contents of the two species are 73.86% and 74.08%, respectively. All tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. The phylogenetic tree is reconstructed using the maximum-likelihood method based on the newly obtained mitochondrial genome sequences and 87 existing mitochondrial genomes of Pentatomoidea from the NCBI database and two species of Lygaeoidea as outgroups. The phylogenetic trees strongly support the following relationships: (Urostylididae + ((Acanthosomatidae + ((Cydnidae + (Dinidoridae + Tessaratomidae)) + (Scutelleridae + Plataspidae))) + Pentatomidae). This study enriches the mitochondrial genome database of Pentatomoidea and provides a reference for further phylogenetic studies.

Secondary structure of the human mitochondrial genome affects formation of deletions

BackgroundAging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions.ResultsBy analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a “hot spot” where one deletion breakpoint occurred within the region of 6–9 kb and another within 13–16 kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11 kb and contacting regions between 6–9 kb and 13–16 kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470–8482 bp (base pair) and a second arm at 13,447–13,459 bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging.ConclusionsOverall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.

The mitochondrial genome of the diploid oat Avena longiglumis

BackgroundAvena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species.ResultsThe complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100–31,235 bp) and medium (144–792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts.ConclusionsComparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.

The mitochondrial and plastid genomes of Oryza sativa L. cv. Taichung 65.

A highly contiguous mitochondrial and plastid genome sequences of a japonica rice cultivar, Taichung 65, were determined by a hybrid approach with long- and short-read sequences. The assembled mitochondrial genome was 465,453 bases in length with an overall GC content of 43.8%. It was predicted to harbor 62 protein-encoding genes, 16 kinds (33 copies) of transfer RNA, and three kinds (six copies) of ribosomal RNA genes. The mitochondrial genome structure in Taichung 65 is largely the same as that of Nipponbare, but the first ∼9.5 kb sequence in Nipponbare (DQ167400) is replaced with a ∼27 kb sequence duplicated from other parts of the mitochondrial genome. Phylogenetic and sequence polymorphism analysis indicated that Taichung 65 is classified as typical japonica. The assembled plastid genome sequence was 134,551 bases in length and completely identical to the previously reported Nipponbare sequence. These near-complete organelle genome sequences will serve as fundamental resources for investigating alloplasmic cytoplasmic male sterile lines and other organelle-controlled phenomena in rice.

Mitochondrial genome analysis, phylogeny and divergence time evaluation of Strixaluco (Aves, Strigiformes, Strigidae).

Background Prior research has shown that the European peninsulas were the main sources of Strixaluco colonisation of Northern Europe during the late glacial period. However, the phylogenetic relationship and the divergence time between S.aluco from Leigong Mountain Nature Reserve, Guizhou Province, China and the Strigiformes from overseas remains unclear. The mitochondrial genome structure of birds is a covalent double-chain loop structure that is highly conserved and, thus, suitable for phylogenetic analysis. This study examined the phylogenetic relationship and divergence time of Strix using the whole mitochondrial genome of S.aluco. New information In this study, the complete mitochondrial genome of Strixaluco, with a total length of 18,632 bp, is reported for the first time. A total of 37 genes were found, including 22 tRNAs, two rRNAs, 13 protein-coding genes and two non-coding control regions. Certain species of Tytoninae were used as out-group and PhyloSuite software was applied to build the ML-tree and BI-tree of Strigiformes. Finally, the divergence time tree was constructed using BEAST 2.6.7 software and the age of Miosurniadiurna fossil-bearing sediments (6.0-9.5 Ma) was set as internal correction point. The common ancestor of Strix was confirmed to have diverged during the Pleistocene (2.58-0.01 Ma). The combined action of the dramatic uplift of the Qinling Mountains in the Middle Pleistocene and the climate oscillation of the Pleistocene caused Strix divergence between the northern and southern parts of mainland China. The isolation of glacial-interglacial rotation and glacier refuge was the main reason for the divergence of Strixuralensis and S.aluco from their common ancestor during this period. This study provides a reference for the evolutionary history of S.aluco.

Comparative Analysis of Complete Mitochondrial Genome of Ariosoma meeki (Jordan and Snider, 1900), Revealing Gene Rearrangement and the Phylogenetic Relationships of Anguilliformes

The mitochondrial genome structure of a teleostean group is generally considered to be conservative. However, two types of gene arrangements have been identified in the mitogenomes of Anguilliformes. In this study, we report the complete mitochondrial genome of Ariosoma meeki (Anguilliformes (Congridae)). For this research, first, the mitochondrial genome structure and composition were analyzed. As opposed to the typical gene arrangement pattern in other Anguilliformes species, the mitogenome of A. meeki has undergone gene rearrangement. The ND6 and the conjoint tRNA-Glu genes were translocated to the location between the tRNA-Thr and tRNA-Pro genes, and a duplicated D-loop region was translocated to move upstream of the ND6 gene. Second, comparative genomic analysis was carried out between the mitogenomes of A. meeki and Ariosoma shiroanago. The gene arrangement between them was found to be highly consistent, against the published A. meeki mitogenomes. Third, we reproduced the possible evolutionary process of gene rearrangement in Ariosoma mitogenomes and attributed such an occurrence to tandem repeat and random loss events. Fourth, a phylogenetic analysis of Anguilliformes was conducted, and the clustering results supported the non-monophyly hypothesis regarding the Congridae. This study is expected to provide a new perspective on the A. meeki mitogenome and lay the foundation for the further exploration of gene rearrangement mechanisms.

Mitochondrial genome of Acheilognathusbarbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis.

Acheilognathusbarbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A.barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome structure and characteristics of this species and constructed a comprehensive phylogenetic tree, based on mitochondrial genome data of several species of Acheilognathus, Rhodeus and Pseudorasboraparva. The complete length of the mitochondrial genome of A.barbatulus is 16726 bp. The genome is a covalently closed double-stranded circular molecule containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a D-loop and a light strand replication initiation region. The base composition of the complete mitochondrial genome is A (29.33%) > T (27.6%) > C (26.12%) > G (16.95%), showing a strong AT preference and anti-G bias. All 13 PCGs have different degrees of codon preference, except for cytochrome c oxidase 1, which uses GTG as the start codon. All the PCGs use ATG as the start codon and the stop codon is dominated by TAG. The encoded amino acids Leu and Ser exist in two types, whereas the rest are all present as one type, except for tRNASer (GCT), which lacks the D-arm and has an incomplete secondary structure, all other tRNAs can be folded to form a typical cloverleaf secondary structure. Based on the 13 PCG tandems, the Maximum Likelihood and Bayesian trees were constructed, based on the concatenated sequence of 13 PCGs for the genera Acheilognathus and Rhodeus, with Pseudorasboraparva as the outgroup. Acheilognathusbarbatulus, Acheilognathustonkinensis and Acheilognathuscf.macropterus were clustered together and the most closely related. The results of this study enrich the mitochondrial genomic data of Acheilognathus and provide molecular and genetic base information for species conservation, molecular identification and species evolution of Acheilognathinae.

Multichromosomal Mitochondrial Genome of Paphiopedilum micranthum: Compact and Fragmented Genome, and Rampant Intracellular Gene Transfer.

Orchidaceae is one of the largest families of angiosperms. Considering the large number of species in this family and its symbiotic relationship with fungi, Orchidaceae provide an ideal model to study the evolution of plant mitogenomes. However, to date, there is only one draft mitochondrial genome of this family available. Here, we present a fully assembled and annotated sequence of the mitochondrial genome (mitogenome) of Paphiopedilum micranthum, a species with high economic and ornamental value. The mitogenome of P. micranthum was 447,368 bp in length and comprised 26 circular subgenomes ranging in size from 5973 bp to 32,281 bp. The genome encoded for 39 mitochondrial-origin, protein-coding genes; 16 tRNAs (three of plastome origin); three rRNAs; and 16 ORFs, while rpl10 and sdh3 were lost from the mitogenome. Moreover, interorganellar DNA transfer was identified in 14 of the 26 chromosomes. These plastid-derived DNA fragments represented 28.32% (46,273 bp) of the P. micranthum plastome, including 12 intact plastome origin genes. Remarkably, the mitogenome of P. micranthum and Gastrodia elata shared 18% (about 81 kb) of their mitochondrial DNA sequences. Additionally, we found a positive correlation between repeat length and recombination frequency. The mitogenome of P. micranthum had more compact and fragmented chromosomes compared to other species with multichromosomal structures. We suggest that repeat-mediated homologous recombination enables the dynamic structure of mitochondrial genomes in Orchidaceae.

Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?-A Case Study of Pulsatilla patens (L.) Mill.

Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD-ccsA, rps4-rps16, and trnL(UAG)-ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes-11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset.

Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework.

Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346562 and 358041bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.

Rapid structural evolution of Dendrobium mitogenomes and mito‐nuclear phylogeny discordances in Dendrobium (Orchidaceae)

AbstractReconstructing mitochondrial genomes of angiosperms is extremely intricate due to frequent recombinations which give rise to varied sized in Dendrobium mitogenomes and their structural variations, even in most orchid species. In this study, we first sequenced two complete and five draft mitochondrial genomes of Dendrobium using next‐generation and third‐generation sequencing technologies. The mitochondrial genomes were 420 538–689 048 bp long, showing multipartite (multichromosomal) structures that consisted of variably sized circular or linear‐mapping isoforms (chromosomes). The comparison of mitochondrial genomes showed frequent gene losses in Dendrobium species. To explore structure variations of mitochondrial genomes in vivo, we quantified copy numbers of five mitochondrial genes and DNA contents per mitochondrion. The gene copy numbers and the DNA contents showed extreme differences during Dendrobium development, suggesting dynamic structures of mitochondrial genomes. Furthermore, phylogenetic relationships of 97 accessions from 39 Dendrobium species were constructed based on 12 nuclear single‐copy genes and 15 mitochondrial genes. We discovered obvious discordance between the nuclear and mitochondrial trees. Reticulate evolution was inferred from the species network analysis in Dendrobium. Our findings revealed the rapid structural evolution of Dendrobium mitochondrial genomes and the existence of hybridization events in Dendrobium species, which provided new insights into in vivo structural variations of plant mitochondrial genomes and the strong potential of mitochondrial genes in deciphering plant evolution history.

Complete Mitogenome Analysis of Five Leafhopper Species of Idiocerini (Hemiptera: Cicadellidae)

Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics, and biogeography. So far, only 12 mitogenomes of the leafhopper tribe Idiocerini have been released in GenBank, although the tribe comprises 488 known species including some agricultural, forestry, and horticultural pests. In order to compare and analyze the mitochondrial genome structure of Idiocerini and even the selective pressure of 13 protein-coding genes (PCGs) of the family Cicadellidae, the complete mitogenomes of five species including Nabicerus dentimus, Sahlbergotettix salicicola, Podulmorinus opacus, Podulmorinus consimilis, and a new species of a new genus were determined by next-generation sequencing. The size of the newly determined mitogenomes ranged from 14,733 bp to 15,044 bp, comprising the standard set of 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a long non-coding control region (CR). The extent of purifying selection presented different pictures in the tribe and the family. The less pronounced genes (0.5 < dN/dS < 1) were nad5 and nad4l in Idiocerin, whereas in the family Cicadellidae including the sequences of Idiocerin, nad1-nad6 and cox1 genes were less pronounced. The codon encoding leucine was the most common in all species, and the codon encoding serine 1 was the most common in all species except for P. opacus. Interestingly, in P. opacus, another of the most common codons is that encoding serine 2. Among the 17 examined species of the Idiocerini, 14 species contained the tandem repeats, and 11 species of them contained the motif "TTATA". These findings will promote research on the structure and evolution of the mitochondrial genome and highlight the need for more mitogenomes in Cicadellidae.

Rearrangement and domestication as drivers of Rosaceae mitogenome plasticity

BackgroundThe mitochondrion is an important cellular component in plants and that functions in producing vital energy for the cell. However, the evolution and structure of mitochondrial genomes (mitogenomes) remain unclear in the Rosaceae family. In this study, we assembled 34 Rosaceae mitogenomes and characterized genome variation, rearrangement rate, and selection signal variation within these mitogenomes.ResultsComparative analysis of six genera from the Amygdaloideae and five from the Rosoideae subfamilies of Rosaceae revealed that three protein-coding genes were absent from the mitogenomes of five Rosoideae genera. Positive correlations between genome size and repeat content were identified in 38 Rosaceae mitogenomes. Twenty repeats with high recombination frequency (> 50%) provided evidence for predominant substoichiometric conformation of the mitogenomes. Variations in rearrangement rates were identified between eleven genera, and within the Pyrus, Malus, Prunus, and Fragaria genera. Based on population data, phylogenetic inferences from Pyrus mitogenomes supported two distinct maternal lineages of Asian cultivated pears. A Pyrus-specific deletion (DEL-D) in selective sweeps was identified based on the assembled genomes and population data. After the DEL-D sequence fragments originally arose, they may have experienced a subsequent doubling event via homologous recombination and sequence transfer in the Amygdaloideae; afterwards, this variant sequence may have significantly expanded to cultivated groups, thereby improving adaptation during the domestication process.ConclusionsThis study characterizes the variations in gene content, genome size, rearrangement rate, and the impact of domestication in Rosaceae mitogenomes and provides insights into their structural variation patterns and phylogenetic relationships.

Complete mitochondrial genome of scorpionfish Scorpaena neglecta (Actinopterygii)

Scorpaena neglecta (Temminck and Schlegel, 1843) is a marine fish, in the family Scorpaenidae, order Scorpaeniformes, class Actinopterygii of the phylum Chordata. The first species of Scorpaena with a complete mitochondrial genome is described in the present study. The circular mitochondrial genome of S. neglecta has 17,202 bp with 54.75% A + T content and encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA). The phylogenetic tree indicates S. neglecta clustered into one branch and is closely related to other Scorpaenidae species. The mitochondrial genome structure and gene content of S. neglecta will support the study of evolution and phylogenetic relationships among Scorpaenidae species.

Improving Environmental DNA Sensitivity for Dreissenid Mussels by Targeting Tandem Repeat Regions of the Mitochondrial Genome

The recent genetic revolution through the analysis of aquatic environmental DNA (eDNA) has become a powerful tool for improving the detection of rare and/or invasive species. For the majority of eDNA studies, genetic assays are designed to target mitochondrial genes commonly referred to as “barcode” regions. However, unlike the typical structure of an animal mitochondrial genome, those for the invasive zebra and quagga mussels are greatly expanded with large extended tandem repeat regions. These sections of repeated DNA can appear hundreds of times within the genome compared to a single copy for the mitochondrial barcode genes. This higher number of target copies per mitochondrial genome presents an opportunity to increase eDNA assay sensitivity for these species. Therefore, we designed and evaluated new eDNA assays to target the extended repeat sections for both zebra and quagga mussels. These assays lower the limit of detection of genomic DNA by 100-fold for zebra mussels and 10-fold for quagga mussels. Additionally, these newly developed assays provided longer durations of detection during degradation mesocosm experiments and greater sensitivity for eDNA detection from water samples collected across western Lake Erie compared to standard assays targeting mitochondrial genes. This work illustrates how understanding the complete genomic structure of an organism can improve eDNA analysis.

The complete mitochondrial genome sequence of the hawkmoth, Ambulyx tobii (Lepidoptera: Sphingidae) and phylogenetic analysis

In this study, we sequenced and analyzed the complete mitochondrial genome of Ambulyx tobii to compare mitochondrial genome structures and reconstruct phylogenetic relationships. The complete mitochondrial genome sequence of A. tobii is circular, 15,343 bp in size and encodes 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region (CR). Nucleotide composition is highly biased toward A + T nucleotides (81.2%). Most PCGs initiate with the standard start codon of ATN and terminate with the typical stop codon TAA/TAG. Phylogenetic analyses were performed using both 13 PCGs and whole mitochondrial genomes showed that A. tobii is closely related to A. substrigilis.

Complex mitogenomic rearrangements within the Pectinidae (Mollusca: Bivalvia)

BackgroundScallops (Bivalvia: Pectinidae) present extraordinary variance in both mitochondrial genome size, structure and content, even when compared to the extreme diversity documented within Mollusca and Bivalvia. In pectinids, mitogenome rearrangements involve protein coding and rRNA genes along with tRNAs, and different genome organization patterns can be observed even at the level of Tribes. Existing pectinid phylogenies fail to resolve some relationships in the family, Chlamydinae being an especially problematic group.ResultsIn our study, we sequenced, annotated and characterized the mitochondrial genome of a member of Chlamydinae, Mimachlamys varia—a species of commercial interest and an effective bioindicator—revealing yet another novel gene arrangement in the Pectinidae. The phylogeny based on all mitochondrial protein coding and rRNA genes suggests the paraphyly of the Mimachlamys genus, further commending the taxonomic revision of the classification within the Chlamydinae subfamily. At the scale of the Pectinidae, we found that 15 sequence blocks are involved in mitogenome rearrangements, which behave as separate units.ConclusionsOur study reveals incongruities between phylogenies based on mitochondrial protein-coding versus rRNA genes within the Pectinidae, suggesting that locus sampling affects phylogenetic inference at the scale of the family. We also conclude that the available taxon sampling does not allow for understanding of the mechanisms responsible for the high variability of mitogenome architecture observed in the Pectinidae, and that unraveling these processes will require denser taxon sampling.

Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians

The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12–19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.

Large Common Mitochondrial DNA Deletions Are Associated with a Mitochondrial SNP T14798C Near the 3′ Breakpoints

Introduction: Large somatic deletions of mitochondrial DNA (mtDNA) accumulate with aging in metabolically active tissues such as the brain. We have cataloged the breakpoints and frequencies of large mtDNA deletions in the human brain. Methods: We quantified 112 high-frequency mtDNA somatic deletions across four human brain regions with the Splice-Break2 pipeline. In addition, we utilized PLINK/Seq to test the association of mitochondrial genotypes with the abundance of these high-frequency mtDNA deletions. A conservative p value threshold of 5E−08 was used to find the significant loci. Results: One mtDNA SNP (T14798C) was significantly associated with mtDNA deletions in two brain regions, the dorsolateral prefrontal cortex (DLPFC) and the superior temporal gyrus. Since the DLPFC showed the most robust association between T14798C and two deletion breakpoints (7816–14807 and 5462–14807), this association was tested in the DLPFC of a replication sample and validated the first results. Incorporating the C allele at 14,798 bp increased the perfect/imperfect length of the repeat at the 3′ breakpoint of the two associated deletions. Conclusion: This is the first study to identify the association of mtDNA SNP with large mtDNA deletions in the human brain. The T14798C allele located in the MT-CYB gene is a common polymorphism that occurs in several mitochondrial haplogroups. We hypothesize that the T14798C association with two deletions occurs by extending the repeat length around the 3′ deletion breakpoints. This simple mechanism suggests that mtDNA SNPs can affect the mitochondrial genome structure, especially in brain where high levels of reactive oxygen species lead to deletion accumulation with aging.