Complete mtDNA Genome Research Articles

The mitochondrial genome of Spualiobarbus curriculus of Pearl River

Spualiobarbus curriculus is an important economic species in China. In this study, the complete mitochondrial genome of S. curriculus collected from three parts of Pearl River is cloned and analyzed. The complete sequence includes 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a D-loop region. The composition of nucleic acid is calculated and it is similar to the known S. curriculus mtDNA. The diversities of sequences and the phylogenetic tree approve that there is high similarity with the one of Yangtze, but there is geographic differences between the sequences. The complete mtDNA genome sequence would contribute to studying phylogenetics in S. curriculus and gemplasm protection of aquatic animal in Pearl River.

Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis).

BackgroundLong-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon’s range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.ResultsBoth laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma.ConclusionsBoth laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1437-0) contains supplementary material, which is available to authorized users.

The complete mitochondrial genome of the Onychostoma gerlachi (Cypriniformes, Cyprinidae)

Onychostoma gerlachi, which belongs to the genus Onychostoma (Cypriniformes, Cyprinidae), is an economic fish that inhabits the flowing freshwater in south of China. The complete mitochondrial genome of O. gerlachi was determined to be 16,601 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. It includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding control region (D-loop). The overall base composition of O. gerlachi is 31.38% for A, 24.24% for T, 28.29% for C and 16.09% for G, with a slight AT bias of 55.62%. The complete mtDNA genome sequence of O. gerlachi obtained in this study provides fundamental data for studying genetic diversity and phylogenetics on this species.

DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals.

Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.

Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations

Heteroplasmy in human mtDNA may play a role in cancer, other diseases, and aging, but patterns of heteroplasmy variation across different tissues have not been thoroughly investigated. Here, we analyzed complete mtDNA genome sequences at ∼3,500× average coverage from each of 12 tissues obtained at autopsy from each of 152 individuals. We identified 4,577 heteroplasmies (with an alternative allele frequency of at least 0.5%) at 393 positions across the mtDNA genome. Surprisingly, different nucleotide positions (nps) exhibit high frequencies of heteroplasmy in different tissues, and, moreover, heteroplasmy is strongly dependent on the specific consensus allele at an np. All of these tissue-related and allele-related heteroplasmies show a significant age-related accumulation, suggesting positive selection for specific alleles at specific positions in specific tissues. We also find a highly significant excess of liver-specific heteroplasmies involving nonsynonymous changes, most of which are predicted to have an impact on protein function. This apparent positive selection for reduced mitochondrial function in the liver may reflect selection to decrease damaging byproducts of liver mitochondrial metabolism (i.e., "survival of the slowest"). Overall, our results provide compelling evidence for positive selection acting on some somatic mtDNA mutations.

Complete mtDNA genomes reveal similar penetrances of maternally inherited type 2 diabetes in two Chinese families

Previous work suggests that mitochondrial DNA (mtDNA) derived from the maternal genome has a close affinity with type 2 diabetes. This would support a familial pattern for type 2 diabetes. Thereby, we analyzed complete mtDNA genomes from two families, A and B, from Southwest China that demonstrated maternally inherited type 2 diabetes. Our data support that mtDNA lineages from families A and B belong to haplogroups A4 and D4h1, respectively. This suggests that maternally inherited type 2 diabetes with similar penetrances can arise in Chinese individuals with strikingly different maternal genetic backgrounds. Two private coding region mutations (G13759A in MT-ND5 and G15930A in tRNA-Thr) were identified in family B. Further evolutionary and phylogenetic analyses suggest that both these mutations have multiple origins and are unlikely to be disease causing.

Two hypotheses of the evolution of endemic sponges in Lake Baikal (Lubomirskiidae)

Complete and nearly complete mtDNA genome sequences were used to resolve differences between two palaeontology-based hypotheses on timing of the origin of the Baikal endemic sponge family Lubomirskiidae (Haplosclerida, Demospongiae). Bayesian ratio test, when coupled with estimates of substitution rates based on known palaeontological findings, provided strong evidence for the Miocene origin over the Late Oligocene one. The common ancestor of the present day sponges in Lake Baikal diverged about 2,3 million years ago (Ma), while Lubomirskia baicalensis, Rezinkovia echinata, Baikalospongia intermedia profundalis and B. bacillifera split in the Pleistocene about 0,7 Ma. A phylogenetic analysis within the family suggested that speciation may have coincided with the occurrence of cold climatic conditions. We argue that the cause of speciation may be niche splitting due to temperature, depth and possibly feeding preferences.

The complete mitochondrial genome sequence of Oceanic whitetip shark, Carcharhinus longimanus (Carcharhiniformes: Carcharhinidae)

The complete mitochondrial DNA sequence of Carcharhinus longimanus was determined and analyzed. The complete mtDNA genome sequence of C. longimanus was 16,706 bp in length. It contained 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and 2 non-conding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of C. longimanus can provide a useful data for further studies on molecular systematics, stock evaluation, taxonomic status and conservation genetics.

Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.

BackgroundComparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias.ResultsWe identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm.ConclusionsThe NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.

Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.

Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs (mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida.

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants.

The majority of genetic studies on Jewish populations have been focused on Ashkenazim, and genetic data from the Sephardic original source, the Iberian Peninsula, are particularly scarce. Regarding the mitochondrial genome, the available information is limited to a single Portuguese village, Belmonte, where just two different lineages (a single one corresponding to 93.3%) were found in 30 individuals. Aiming at disclosing the ancestral maternal background of the Portuguese Jewry, we enlarged the sampling to other crypto-Jewish descendants in the Bragança district (NE Portugal). Fifty-seven complete mtDNA genomes were newly sequenced and - in contrast with Belmonte - a high level of diversity was found, with five haplogroups (HV0b, N1, T2b11, T2e and U2e) being putatively identified as Sephardic founding lineages. Therefore - in sharp contrast with Belmonte - these communities have managed to escape the expected inbreeding effects caused by centuries of religious repression and have kept a significant proportion of the Sephardic founder gene pool. This deeper analysis of the surviving Sephardic maternal lineages allowed a much more comprehensive and detailed perspective on the origins and survival of the Sephardic genetic heritage. In line with previously published results on Sephardic paternal lineages, our findings also show a surprising resistance to the erosion of genetic diversity in the maternal lineages.

The characterization of goat genetic diversity: Towards a genomic approach

The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers for each of the main livestock species, FAO has promoted the meta-analysis of local datasets, to achieve a global view of molecular genetic diversity. Analysis within the EU Globaldiv project of two large goat microsatellite datasets produced by the Econogene Consortium and the IAEA CRP–Asia Consortium, respectively, has generated a picture of goat diversity across continents. This indicates a gradient of decreasing diversity from the domestication centre towards Europe and Asia, a clear phylogeographic structure at the continental and regional levels, and in Asia a limited genetic differentiation among local breeds. The development of SNP panels that assay thousands of markers and the whole genome sequencing of livestock permit an affordable use of genomic technologies in all livestock species, goats included. Preliminary data from the Italian Goat Consortium indicate that the SNP panel developed for this species is highly informative. The existing panel can be improved by integrating additional SNPs identified from the whole genome sequence alignment of goats adapted to extreme climates. Part of this effort is being achieved by international projects (e.g. EU FP7 NextGen and 3SR projects), but a fair representation of the global diversity in goats requires a large panel of samples (i.e. as in the recently launched 1000 cattle genomes initiative). Genomic technologies offer new strategies to investigate complex traits difficult to measure. For example, the comparison of patterns of diversity among the genomes in selected groups of animals (e.g. adapted to different environments) and the integration of genome-wide diversity with new GIScience-based methods are able to identify molecular markers associated with genomic regions of putative importance in adaptation and thus pave the way for the identification of causative genes. Goat breeds adapted to different production systems in extreme and harsh environments will play an important role in this process. The new sequencing technologies also permit the analysis of the entire mitochondrial genome at maximum resolution. The complete mtDNA sequence is now the common standard format for the investigation of human maternal lineages. A preliminary analysis of the complete goat mtDNA genome supports a single Neolithic origin of domestic goats rather than multiple domestication events in different geographic areas.

Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.

Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000–5000 years, reaching different parts of southern Africa 1200–2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speakers. During their expansion, Bantu speakers would have come into contact with diverse local populations, such as the Khoisan hunter-gatherers and pastoralists of southern Africa, with whom they may have intermarried. In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia, and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations. Only the pastoralist Himba and Herero stand out due to high frequencies of particular L3f and L3d lineages; the latter are also found in the neighboring Damara, who speak a Khoisan language and were foragers and small-stock herders. In contrast, the close cultural and linguistic relatives of the Herero and Himba, the Kuvale, are genetically similar to other Bantu-speakers. Nevertheless, as demonstrated by resampling tests, the genetic divergence of Herero, Himba, and Kuvale is compatible with a common shared ancestry with high levels of drift, while the similarity of the Herero, Himba, and Damara probably reflects admixture, as also suggested by linguistic analyses.

The complete mitochondrial genome of Discogobio tetrabarbatus (Cypriniformes Cyprnidae)

The complete mitochondrial genome of a China endemic fish Discogobio tetrabarbatus is a circular molecular of 16,596 bp in size, containing 13 protein-coding genes(PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region. Most of the genes are encoded on the heavy strand, expect for ND6 and eight tRNAs. The control region is 936 bp in length and located between the tRNAPro and tRNAPhe genes. Of 13 PCGs, 7 genes (ND2, COII, ATPase 6, COIII, ND3, ND4, Cytb) had an incomplete stop codon. The complete mtDNA genome sequence obtained in this study would be useful for studying genetic diversity and phylogenetics in Discogobio tetrabarbatus and related taxa in future.

The complete mitochondrial genome of the ratmouth barbell, Ptychidio jordani (Cypriniformes Cyprnidae)

The complete mitochondrial genome of an endemic fish Ptychidio jordani is a circular molecular of 16,602 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region. Most of the genes are encoded on the heavy strand, expect for ND6 and eight tRNAs. The control region is 940 bp in length and is located between the tRNAPro and tRNAPhe genes. Of 13 PCGs, 7 genes (ND2, COII, ATPase 6, COIII, ND3, ND4, Cytb) had an incomplete stop codon. The complete mtDNA genome sequence obtained in this study would be useful for studying genetic diversity and phylogenetics in Ptychidio jordani and related taxa in future.

Complete mitochondrial genome of Pareuchiloglanis sinensis (Siluriformes: Sisoridae)

The complete mitochondrial genome of Pareuchiloglanis sinensis, an endemic Chinese sisorid fish, was determined by DNA sequencing based on the PCR fragments. The complete mtDNA genome sequence of P. sinensis is 16,593 bp in length, with a gene content of 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and a typical gene arrangement identical to many other reported fishes. The overall base composition of the heavy strand was 30.6% A, 24.2% T, 16.0% G and 29.2% C, with a relatively high A + T content (54.8%). This will provide a useful tool for understanding the genetic diversity, population structure and conservation status of P. sinensis in future.

The rise and fall of a genus: Complete mtDNA genomes shed light on the phylogenetic position of yellow-tailed woolly monkeys, Lagothrix flavicauda, and on the evolutionary history of the family Atelidae (Primates: Platyrrhini)

Using complete mitochondrial genome sequences, we provide the first molecular analysis of the phylogenetic position of the yellow-tailed woolly monkey, Lagothrix flavicauda (a.k.a. Oreonax flavicauda), a critically endangered neotropical primate endemic to northern Perú. The taxonomic status and phylogenetic position of yellow-tailed woolly monkeys have been debated for many years, but in this study both Bayesian and maximum likelihood phylogenetic reconstructions unequivocally support a monophyletic woolly monkey clade that includes L. flavicauda as the basal taxon within the radiation. Bayesian dating analyses using several alternative calibrations suggest that the divergence of yellow-tailed woolly monkeys from other Lagothrix occurred in the Pleistocene, ∼2.1Ma, roughly 6.5 my after the divergence of woolly monkeys from their sister genus, Brachyteles. Additionally, comparative analysis of the cytochrome oxidase subunit 2 (COX2) gene shows that genetic distances between yellow-tailed woolly monkeys and other Lagothrix from across the genus’ geographic distribution fall well within the range of between-species divergences seen in a large number of other platyrrhine primate genera at the same locus and outside the range of between-genus divergences. Our results thus confirm a position within Lagothrix for the yellow-tailed woolly monkey and strongly suggest that the name Oreonax be formally considered a synonym for this genus. This revision in taxonomic status does not change the dire conservation threats facing the yellow-tailed woolly monkey in Perú, where the remaining wild population is estimated at only ∼10,000 individuals living in a highly fragmented landscape.

The complete mitochondrial genome of Pseudobagrus emarginatus (Siluriformes: Bagridae)

In this study, the total mitochondrial genome sequence of Pseudobagrus emarginatus (Siluriformes: Bagridae) was firstly sequenced and determined. The complete mtDNA genome sequence of P. emarginatus is 16,534 bp in length. It consists of 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a non-coding control region (D-loop). The overall-based composition was 31.5% A, 26.8% T, 14.9% G and 26.8% C, with a high A+T content (58.3%), which was nearly the same as other reported catfishes. These results will provide useful data to the natural resources conservation and systematics analysis of P. emarginatus and its related species in future.

Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.

The complete mitochondrial genome of the spotted longbarbel catfish, Hemibagrus guttatus (Siluriformes, Bagridae)

Spotted longbarbel catfish, Hemibagrus guttatus (Siluriformes, Bagridae), is regarded as one of the “four famous fish” in the Pearl River system in China. So far, very few genomic resources from this species were available. In the present study, the complete mitochondrial genome of H. guttatus was determined to be 16,528 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. It includes 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a non-coding control region (D-loop). The complete mtDNA genome sequence obtained in this study would be useful for studying genetic diversity and phylogenetics in H. guttatus and related taxa in future.