Complete Mitochondrial DNA Genome Sequences Research Articles

The complete mitochondrial genome of the freshwater fish Traccatichthys pulcher (Cypriniformes: Nemacheilidae) from China

This study aimed to sequence and annotate the complete mitochondrial DNA genome sequence of Traccatichthys pulcher. The mitochondrial genome comprised 16,583 bp, harboring 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The whole genome contained T (25.8%), C (26.9%), A (31.4%), and G (15.9%), showing an obvious AT bias (57.2%). Based on the concatenated protein sequences of 13 PCGs, a phylogenetic tree was reconstructed by the maximum likelihood method, and the topology revealed the monophyly of Traccatichthys, and the gathering of T. pulcher and M. pulcher. The mitochondrial DNA of T. pulcher (MZ853162.1) and M. pulcher (NC_031581.1) were aligned by the BLAST 2 sequences tool, which showed 97% similarity.

Characterization of the complete mitochondrial genome and phylogenetic analysis of Opsarius pulchellus (Cypriniformes, Danionidae, Chedrinae)

This study aimed to sequence and annotate the complete mitochondrial DNA genome sequence of Opsarius pulchellus. Complete mitochondrial genome is a circular molecule of 16,552 bp in length, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a displacement loop region. Proportion of nucleotides in mitochondrial genome is 26.8% T, 26.9% C, 27.6% A, and 18.8% G, with an AT bias of 54.4%. Maximum-likelihood phylogenetic tree was reconstructed using the connected protein sequences of 13 PCGs of O. pulchellus and other 18 fishes. Result of phylogenetic analysis supports a close relationship between O. pulchellus and Barilius bendelisis (Hamilton, 1807). Fundamental genetic data of O. pulchellus would be beneficial for further studies on genetic diversity and phylogeny.

Characterization of a complete mitochondrial genome of Turdus ruficollis (Passeriformes: Turdidae)

Turdus ruficollis is mainly found in China and Northeast Asia. So far, the mitochondrial genome of more than 20 species from the genus Turdus has been studied. However, the relevant information of T. ruficollis has not been reported. To grasp a better comprehension on the molecular basis of T. ruficollis, we obtained the complete mitochondrial DNA genome sequences of this species. The mitogenome was 16,737 bp in length, which consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. A phylogenetic tree based on complete mitogenome sequences revealed that, within the genus Turdidae, T. ruficollis is closely related to T. naumanni and T. eumomus. The complete mitochondrial genome of T. ruficollis would be of great utility for population genetics and phylogeography of the Turdidae family and would also provide meritorious insights for future studies on conservation, genetics, and phylogeny of the Passeriformes family.

Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of Penaeus sensu lato.

Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome‐wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.

Ancient DNA from Guam and the peopling of the Pacific

Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.

The sequence and characterization of mitochondrial of Lepus oiostolus (Lagomorpha: Leporidae)

Lepus oiostolus is widely inhabited in the Qinghai-Tibet Plateau. So far, little mitochondrial genome information of this genus has been described. To grasp a better comprehension on the molecular basis of L. oiostolus, we obtained the complete mitochondrial DNA genome sequences of this species. The mitogenome was 17,320 bp in length, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 noncoding regions. The complete mitochondrial genome of L. oiostolus would be of great utility in the phylogenetic analysis of the Lagomorpha and also provide meritorious insights into the deeper problems of the phylogenic analysis.

The complete mitochondrial genome of the Gymnocypris scleracanthus (Cypriniformes: Cyprinidae)

The Gymnocypris scleracanthus, a species of genus Gymnocypris belongs to Schizothoracinaein Cyprinidae. In this study, the complete mitochondrial DNA genome sequence of G. scleracanthus was determined. The 16,771 bp long circular molecule contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and two non-coding regions, showing a typical vertebrate pattern. These genes except ND6 and eight tRNA genes were encoded on the H-strand. Phylogenetic analysis showed that the G. scleracanthus was a part of genus Gymnocypris and had closer relationship with Gymnocypris dobula and was independent from other species of Psilorhynchus and Labeoninae in Cyprinidae.

The complete mitochondrial genome of Xenophysogobio nudicorpa (Cypriniformes; Cyprinidae)

In this study, the complete mitochondrial DNA genome sequence of Xenophysogobio nudicorpa was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of X. nudicorpa is a circular molecule of 16,616 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of X. nudicorpa is 30.5% A, 26.0% C, 16.8% G, and 26.7% T, with a relatively high A+T content (57.2%). The results could provide useful data for studying genetic diversity and phylogenetics in X. nudicorpa and related species.

The complete mitochondrial genome of Sinibrama taeniatus (Cyprinidae: Cultrinae)

In this study, the complete mitochondrial DNA genome sequence of Sinibrama taeniatus was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of S. taeniatus was a circular molecule of 16,623 bp in length. It consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of S. taeniatus was 31.3% A, 26.8% C, 16.1% G, and 25.8% T, with a relatively high A + T content (57.1%). The results could provide useful data for studying genetic diversity and phylogenetics in S. taeniatus and related species.

The complete mitochondrial genome sequence of Chuanchia labiosa (Cypriniformes: Cyprinidae)

Chuanchia labiosa Herzenstein, 1891 (Cyprinidae: Schizothoracinae) is the sole species of genus Chuanchia and is endemic to China. This species plays an important role in the upper reaches of the Yellow River and has been listed in both the China Red Data Book of Endangered Animal and the China Species Red List. In this study, the complete mitochondrial DNA genome sequence of C. labiosa was determined. The mitogenome is 16,705 bp in length, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Overall basic composition of mitochondrial genome of C. labiosa is 28.39% for A, 27.16% for T, 26.09% for C, and 18.36% for G with a slightly high A + T content (55.55%). The complete mitogenome sequence of C. labiosa would be useful for stock evaluation and further conservation genetic studies for this endangered species.

The complete mitochondrial genome sequence of Platypharodon extremus (Cypriniformes: Cyprinidae)

Platypharodon extemus is a monotypic species of Schizothoracine fishes and it was listed as Endangered species in the “China Red Data Book (Pisces)”, Vulnerable (V) by the National Environmental Protection Agency and Endangered Species Scientific Commission. So far, little mitochondrial genome information of this genus has been described. In this study, we obtained the complete mitochondrial DNA genome sequences of this species. The mitogenome was 16,668 bp in length, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 noncoding regions. The base composition of this mitochondrial genome was 28.6% A, 27.3% T, 18.2% G, 25.9% C, with a high A + T content (55.9%). The complete mitochondrial genome of P. extremus would be of great utility in the phylogenetic analysis of the schizothoracine fishes and also provide meritorious insights into the deeper problems of the phylogenic analysis.

Characterization of the complete mitochondrial genome sequence of Homatula potanini (Cypriniformes, Nemacheilidae, Nemachilinae)

Homatula potanini is an endemic and one of ornamental fishes in the upper stream of the Yangtze River and its tributaries. However, wild populations of H. potanini declined sharply due to anthropological activity in the Jinsha River during the past decades. In present study, the complete mitochondrial DNA genome sequence of H. potanini was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial genome sequence is a circular molecule of 16,569 bp in size. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of H. potanini is 30.1% A, 26.9% C, 16.7% G, and 26.3% T, with a relatively high A + T content (56.4%). The results could provide useful data for studies on genetic structure and rational resource conservation in H. potanini.

The complete mitochondrial genome sequence of Triplophysa anterodorsalis (Teleostei, Balitoridae, Nemacheilinae)

Triplophysa anterodorsalis is an endemic fish in the upper stream of the Yangtze River, Jinsha River and its tributaries. However, wild populations of T. anterodorsalis declined sharply due to cascade hydropower stations constructed successively in the Jinsha River during the past decades. In the present study, the complete mitochondrial DNA genome sequence of T. anterodorsalis was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial genome sequence of T. anterodorsalis is a circular molecule of 16,567 bp in size. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of T. anterodorsalis is 27.37% A, 25.68% C, 18.37% G, and 28.57% T, with a relatively a relatively high A + T content (55.94%). The results could provide useful data for studies on genetic structure and diversity and rational resource conservation in T. anterodorsalis.

The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina): a unique gene arrangement and its phylogenetic implications.

Meloidogyne graminicola is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of Pratylenchus vulnus (21,656 bp). The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of M. graminicola contains 36 genes (lacking atp8) that are transcribed in the same direction. The gene arrangement of the mt genome of M. graminicola is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while tRNASer(AGN) lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by tRNASer(UCN). Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea. In the clade of Tylenchoidea, M. graminicola is sister to P. vulnus, and H. glycines is sister to R. similis, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.

The complete mitochondrial genome of Schizothorax chongi (Fang, 1936) (Teleostei, Cyprinidae, Schizothoracinae)

Schizothorax chongi is an endemic and important polyploidy fish in the upper stream of the Yangtze River. S. chongi represents a typical model species to study historical adaptation and evolution in the Tibetan Plateau. In this study, the complete mitochondrial DNA genome sequence of S. chongi was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of S. chongi is a circular molecule of 16,584 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of S. chongi is 29.6% A, 27.1% C, 17.9% G, and 25.4% T, with a high AT content (55.0%). The results could provide useful data for further studies on phylogenetics, conservation genetics and rational resource management for S. chongi.

Early Austronesians: Into and Out Of Taiwan

A Taiwan origin for the expansion of the Austronesian languages and their speakers is well supported by linguistic and archaeological evidence. However, human genetic evidence is more controversial. Until now, there had been no ancient skeletal evidence of a potential Austronesian-speaking ancestor prior to the Taiwan Neolithic ~6,000 years ago, and genetic studies have largely ignored the role of genetic diversity within Taiwan as well as the origins of Formosans. We address these issues via analysis of a complete mitochondrial DNA genome sequence of an ~8,000-year-old skeleton from Liang Island (located between China and Taiwan) and 550 mtDNA genome sequences from 8 aboriginal (highland) Formosan and 4 other Taiwanese groups. We show that the Liangdao Man mtDNA sequence is closest to Formosans, provides a link to southern China, and has the most ancestral haplogroup E sequence found among extant Austronesian speakers. Bayesian phylogenetic analysis allows us to reconstruct a history of early Austronesians arriving in Taiwan in the north ~6,000 years ago, spreading rapidly to the south, and leaving Taiwan ~4,000 years ago to spread throughout Island Southeast Asia, Madagascar, and Oceania.

The complete mitochondrial genome sequence of Pseudobagrus ussuriensis (Siluriformes: Bagridae)

The complete mitochondrial DNA genome sequence of Ussuri catfish (Pseudobagrus ussuriensis) was determined. The mitochondrial genome sequence is a circular molecule with 16,536 bp in length. It contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The nucleotide acid composition of the entire mitogenome is 31.79% for A, 26.84% for T, 14.87% for G, and 26.50% for C, showing a high A+T content. The complete mitogenome sequence of P. ussuriensis can be used in the studies on molecular systematics, conservation genetics, and stock evaluation.

The complete mitochondrial genome sequence of Schizothorax macropogon (Cypriniformes: Cyprinidae)

Schizothorax macropogon is listed as Near Threatened species in International Union for Conservation of Nature Red List. It is restrictly distributed in the Yarlung Zangbo (upper Brahmaputra) River in Tibet, China. Till now, little is known about the mitochondrial genome information of this species. In this study, the complete mitochondrial DNA genome sequence of S. macropogon was determined. The mitogenome is a circular molecule of 16,588 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 noncoding regions. Overall base composition of mitochondrial genome of S. macropogon was 29.82% A, 26.94% C, 17.74% G, and 25.50% T, with a high A+T content (55.32%). The complete mitogenome sequence of S. macropogon can be used in the studies on molecular systematics, phylogeography, stock evaluation, and conservation genetics.

Complete mitochondrial DNA genome sequences from the first New Zealanders

The dispersal of modern humans across the globe began ~65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.

The complete mitochondrial genome sequence of Rastrelliger kanagurta (Perciformes: Scombridae)

In this study, the complete mitochondrial DNA genome sequence of Rastrelliger kanagurta has been determined. The mitogenome was 16,537 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions. The A+T content of the mitochondrial genome of R. kanagurta was 52.29%, and the content was 26.92% for A, 30.67% for C, 17.03% for G, and 25.37% for T. The complete mitogenome of R. kanagurta can provide an important data for the studies on molecular systematics, species identification, stock evaluation, conservation genetics, and evolutionary adaptation mechanisms.