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The Asiatic softshell turtle, also known as the black-rayed softshell turtle (Amyda cartilaginea; Accession no: MT039230), is found in northeastern India (Mizoram), Brunei Darussalam, Indonesia, Malaysia, Singapore, Myanmar, Laos, Vietnam, Cambodia, and Thailand. This turtle is thought to have been introduced into the Sunda Islands, Sulawesi, and Yunnan, China, through the Malay Peninsula to Sumatra, Java, and Borneo. Herein, we determined the complete mitochondrial genome of A. cartilaginea for the first time using next-generation sequencing (NGS). The assembled mitogenome was 16,763 bp in length and encoded 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), and one control region (CR). The PCGs based maximum-likelihood phylogeny discriminated A. cartilaginea from other Testudines and clusters within family Trionychidae with the sister taxa of Nilssonia nigricans.

The goral (Naemorhedus caudatus), a species of the Caprinae, is classified as globally vulnerable on the IUCN Red List of Threatened Species because of its sharply declining population size, which is attributable to habitat destruction. In this study, we determined and described the complete mitochondrial genome of N. c. griseus, a goral subspecies from the western Sichuan of China; the mitochondrial genome of this goral is 16,557 bp in length (GenBank accession No: MG865962) and contains 13 protein-coding genes (PCGs), two rRNA genes, 23 tRNA genes, and one control region (D-loop). Ten PCGs start with ATG, but ND2, ND3, and ND5 use ATA as the start codon. The overall base composition of the mitochondrial DNA is 34.6% A, 28.6% T, 22.4% C, and 14.4% G. The G+C content is 36.8%. Phylogenetic analysis revealed that N. c. griseus clustered into a clade with other Naemorhedus species with high bootstrap support. This work provides additional molecular information for studying the conservation genetics and evolutionary relationships of this endangered species.

The white-lipped deer (Cervus albirostris) is a rare and endangered species endemic to the Qinghai–Tibet Plateau in China. In this study, we determined the complete mitochondrial genome sequence of the white-lipped deer. The total length of the mitogenome is 16473 bp. It has the typical structure of a vertebrate mitochondrial genome including 13 protein-coding genes(PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region (D-loop). tRNASer lacks the stem of the dihydrouridine (DHU) arm and fails to form a typical cloverleaf secondary structure. A phylogenetic tree based on the 13 PCG sequences of nine species closely related to white-lipped deer shows the classification status of the species within the family Cervidae. These results provide new molecular biology information to further understand the diversity of the white-lipped deer, which will help to protect this population.

The Sichuan deer (Cervus elaphus macneilli) is a rare animal native to western Sichuan and southeastern Tibet, China. In this study, the entire Sichuan deer mitochondrial genome was sequenced; it was 16350 bp long (GenBank accession No: KX449334) and contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region (D-loop). Ten PCGs started with ATG, but ND2, ND3, and ND5 used ATA as the start codon. PCG homology between C.e.macneilli and four other red deer subspecies ranged from 93.9 to 96%, which indicates a clear difference among subspecies. Phylogenetic analysis revealed that the Sichuan deer clustered into a clade with other red deer subspecies with high bootstrap support. This work provides additional molecular information for studying red deer conservation genetics and evolutionary relationships.

Forest musk deer (FMD) is an endangered species, and its population size has dropped dramatically. In this study, we determined the complete mitochondrial genome of a FMD. The genome was 16,353 bp long, and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region. Most PCGs were distributed on the heavy strand except ND6 and eight tRNA genes, which were encoded on the light strand. The nucleotide composition was asymmetric, with an overall A+T content of 62.1%. Comparison with one previously described mitochondrial genome revealed 94.4% sequence homology and 1128 nucleotide mutation sites, which represents a substantial difference. A phylogenetic tree based on Cytb genes of eight closely related musk deer species showed that our sample clustered with two FMD subspecies from Yunnan, China. These results provide novel molecular information that can potentially be used for genetic diversity conservation of this species.

The Vietnam Warty Newt (Paramesotriton deloustali) is threatened by habitat loss and illegal capture for traditional medicines use and domestic pet trade. In this study, we described the complete mitochondrial genome (mitogenome) of P. deloustali. The entire mitogenome sequence of P. deloustali is 16,391 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region and an additional 261 bp non-coding sequence between tRNAThr and tRNAPro genes. Our new data of the complete mitogenome of P. deloustali will offer solid genetic information for further conservation genetics research of this threatened species.

Trachypithecus poliocephalus : (Primates: Cercopithecidae), classified as critically endangered (IUCN) and in China was listed National First Class Protected Animal. In this study, the complete mitochondrial genome sequence of T. poliocephalus has been reported for the first time in China. The complete mitochondrial genome of T. poliocephalus was sequenced and it contained 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and one control region (D-loop).

We newly obtained the near complete mitochondrial genome of Oreolalax schmidti (18,481bp) by using polymerase chain reaction (PCR) in this study. It includes 13 protein-coding genes (PCG), two ribosomal RNA (rRNA) genes, and 23 transfer RNA (tRNA) genes. The phylogenetic tree indicates that the Oreolalax schmidti is closely related to the O. lichuanensis. This report will help the further studies of Oreolalax species classification and source protection.

A complete mitogenome sequence of the blue-crested lizard (Calotes mystaceus) was determined in this study. The 16,506 bp genome consists 13 protein-coding genes (PCG), two ribosomal RNA (rRNA) gen...

The complete mitochondrial genome of the Oreolalax major (17,786 bp long) was obtained in this study. It includes 13 protein-coding genes (PCG), two ribosomal RNA (rRNA) genes, and 23 transfer RNA (tRNA) genes (GenBank accession number MN803320). The phylogenetic tree indicates that the O. major is closely related to the O. xiangchengensis.

Ferret-badger (Melogale moschata) is a widely distributed and rarely studied species. Therefore, we sequenced its complete mitochondrial genome, which is circular in shape with 16,511 bp length and have a structure typical to mammals. There is 98.67% similarity when compared with the reported sequence (HM106328). It contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control regions (D-loop). This study can provide novel molecular information and genetic diversity of ferret-badger.

Red-and-white giant flying squirrel (Petaurista alborufus) is a widely distributed but rarely studied species. Here, we sequenced the complete mitochondrial genome about it, which is a circular genome of 16,511 bp and have a typical structure with mammals. The base composition shows higher composition of A\T. There are 61 variations and eight base deletions between two sequences when compared with the reported sequence (JQ743657). In this study, we obtain a new mitochondrial genome sequence of red-and-white giant flying squirrel, which provide novel molecular information that could prove fundamental to our understanding of diversity research and phylogenetic structure.

The complete mitochondrial of Cynops cyanurus cyanurus was determined by using Sanger sequencing and the mitogenome size of C. c. cyanurus was 16,465 bp. It contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, 1 control region (D-loop) and a non-coding region (NC). In addition, the phylogenetic tree shows that C. c. cyanurus has the closest relationship with C. c. chuxiongensis. Hoping this study can improve our understanding of the species evolutionary relationship of Cynops.

Due to the multiple causes, the population of roe deer has declined significantly. In this study, we analyzed the complete mitogenome of Capreolus pygargus bedfordi, whose genome was 16,357 bp long. There were 13 protein-coding genes (PCG), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes, and one control region. Nine PCGs started with ATG, while NAD2, NAD3, and NAD5 genes commenced with ATA, and ND4L began with GTG. ND6 and eight tRNA genes were encoded on the L-strand. These results provide newer molecular information, which contribute to its molecular and phylogenetic studies, and genetic diversity conservation.

In this study, the complete mitochondrial genome sequence of Prionodon pardicolor pardicolor has been reported for the first time in China. The total length of the mitogenome was 16,689 bp. It contained the typical structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). tRNASer lost the stem of DHC loop and failed to form a typical cloverleaf secondary structure. Mitochondrial control region of P. p. pardicolor was 1242 bp long, laying between the tRNAPro and tRNAPhe genes. Based on the 13 PCG sequences, homology and single-nucleotide mutation loci were performed between P. p. pardicolor and P. pardicolor. As a result, the homology between two species was 99.6% on average, and Nucleotide mutation loci was 41. Also, in view of their mitochondrial control region comparison, P. p. pardicolor drop 28 bp nucleotides.

Cynops cyanurus chuxiongensis is distributed in Yunnan plateau. In this paper, we sequenced and determined the complete mitochondrial genome of C. c. chuxiongensis. The assembled mitogenome is 16,4...

In this study, we sequenced the complete mitochondrial genome of Argali sheep (Ovis ammon). The total length was 16,612 bp, which contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). Eight tRNA genes with one PCG (ND6) encoded on the L-strand, others were encoded on the H-strand. The neighbor-joining analysis shows that Argali sheep has a close relationship with the same genus species of Ovis aries and Ovis orientalis. This study has provided new data for the phylogeny of Argali sheep.

The mitochondrial genome (mitogenome) sequence of the tree frogPolypedates megacephalus(16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome ofP. megacephalus(19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.

Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies.

Rhesus macaques are raised in almost every Chinese zoo due to their likeability and ease in feeding; however, little is yet known about the genetic diversity of rhesus macaques in captivity. In this study, a 475-base pair nucleotide sequence of the mitochondrial DNA control region was obtained from the fecal DNA of 210 rhesus macaque individuals in captivity. A total of 69 haplotypes were defined, 51 of which (73.9%) were newly identified. Of all haplotypes, seven were shared between two zoos, and 62 haplotypes (89.8%) appeared only in a specific zoo, indicating a low rate of animal exchange between Chinese zoos. Moreover, there was a relatively high level of genetic diversity among the rhesus macaques (Hd = 0.0623 ± 0.0009, Pi = 0.979 ± 0.003,K= 28.974). Phylogenetic analysis demonstrated that all haplotypes were clearly clustered into two major haplogroups—Clade A (southeastern China) and Clade B (southwestern China)—and each major clade contained several small sub-haplogroups. The haplotypes of rhesus macaques from the same zoo were not clustered together for the most part, but scattered among several subclades on the phylogenetic tree. This indicates that the rhesus macaques in most Chinese zoos may originat from a diverse collection of geographical areas. Our results demonstrate that zoos play an important role in the conservation of the genetic diversity of rhesus macaques, as well as provide useful information on the genetic management of captive rhesus macaques.

Tylototriton shanorum, an endemic species of Myanmar, is threatened by illegal capture and environmental destruction. Here, the complete mitochondrial genome (mitogenome) of T. shanorum is described. The entire mitogenome sequence of T. shanorum is 17,096 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region. In addition, two additional 3′ Cytb like sequences and two complete tRNAThr genes, one pseudo tRNAThr, and three noncoding sequences (NC1, NC1′ and NC2) were situated between Cytb and tRNAPro genes. The new complete mitogenome sequence of T. shanorum will be useful for conservation genetics, evolutionary biology, phylogeography, as well as phylogenetic relationships studies of this threatened species.

The Oriental Fire-bellied Newt (Cynops orientalis David) has been listed as Near Threatened species (NT) recently due to habitat destruction and degradation and illegal trade in the domestic and international pet markets. We sequenced and characterized the complete mitochondrial genome (mitogenome) of C. orientalis in this paper. The complete mitogenome sequence of C. orientalis is 16,294 bp in length, containing 37 genes (13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes and one control region). The new sequenced complete mitogenome of C. orientalis will provide useful information for application in conservation genetics and evolution for this near threatened species.

Grey-headed Parrotbill, Paradoxornis gularis, has significant economic and scientific value in China. Length of the complete mitochondrial genome of grey-headed parrotbill is 17,743 bp, and it contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and a D-loop sequence. The overall base composition of the mitochondrial sequence was 29.47% A, 14.68% G, 24.33% T, 31.52% C. All tRNAs have the typical cloverleaf structure, except for tRNASer. All PCGs start with ATG codons, except for COXI and NADH6, which are initiated by GTG and CTA, respectively.

The complete mitochondrial genome of tufted deer (Elaphodus cephalophus) has been described in our research. The sequence of this genome is 16356 bp with a circular structure, and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region. When compare with the reference sequence (DQ873526), it shows that there are 262 variations, 4 base deletions and 13 base insertions. In this study we obtain a new complete mitochondrial genome sequence of tufted deer that provide effective molecular information for the diversity research and phylogenetic structure.

We obtained the complete mitochondrial genome of Amolops granulosus, which was 17,785 bp in length and it contained the 37 typical mitochondrial genes: 2 ribosomal RNAs, 22 transfer RNAs (tRNAs), 1...

Blue-winged Minla is a small-sized bird, belonging to the Family Leiothrichidae of the Passeriformes. The population is suspected to be in decline owing to ongoing habitat destruction and fragmentation. Therefore, we sequenced and analyzed the Blue-winged Minla mitochondrial genome to provide a theoretical basis for protecting the brids. The mitochondrial genome of Blue-winged Minla was 17862 bp, it contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 control regions. The overall base composition of the mitochondrial was 30.88% A, 13.82% G, 23.86% T, 31.44% C.

In this study, we determined the complete mitochondrial genome sequence of the Mustela sibirica. The complete mitogenome of M. sibirica is 16,529 bp in length and consist of 13 protein-coding genes...

In this study, we reported the complete mitochondrial genome sequence of a red panda (Ailurus fulgens). The mitogenome (GenBank accession number MK886830) length is 16,517 bp and exhibits the typic...

The complete mitochondrial genome of Chinese serow (Capricornis milneedwardsii) has been described. It is a circular genome of 16,441 bp with a higher A + T content of 60.25%. By reconstructing a M...

In China, the stripe-throated yuhina is mainly distributed in southwestern and the population is not abundant. In this study, we sequenced and characterized its complete mitochondrial genome. The c...

In this study, we described the complete mitochondrial genome of Alpine musk deer (Moschus chrysogaster) from China. It has a circular genome of 16,352 bp (GeneBank number: MK697349) with a higher ...

We determined the complete mitochondrial genome of the tree frog, Polypedates braueri using next generation sequencing (NGS) and Sanger sequencing. The mitogenome of P. braueri was 19,904 bp in len...

The complete mitochondrial of Black-chinned Yuhina is 17,817 bp in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 control regions. The overall base composit...

The dwarf blue sheep (Pseudois schaeferi) belongs to the subfamily Caprinae within the Cetartiodactyla. Here, we report on the complete mitochondrial genome of a dwarf blue sheep from Nangqian of Q...

The blue sheep (Pseudois nayaur) belongs to the subfamily Caprinae. Here, we report the complete mitochondrial genome of a blue sheep subspecies (Pseudois nayaur szechuanensis) from Gongga Mountain...

Adaptive evolutions to high-altitude adaptation have been intensively studied in mammals. However, considering the additional vertebrate groups, new perception regarding selection challenged by high-altitude stress on mitochondrial genome can be gained. To test this hypothesis, we compiled and analyzed the mitochondrial genomes of 5 alpine pheasants and 12 low-altitude species in Phasianidae. The results that evolutionary rates of ATP6 and ND6 showing significant fluctuation among branches when involved with five alpine pheasants revealed both genes might have implications with adapting to highland environment. The radical physico-chemical property changes identified by the modified MM01 model, including composition (C) and equilibrium constant (ionization of COOH) (Pk') in ATP6 and beta-structure tendencies (Pβ), Pk', and long-range non-bonded energy (El) in ND6, suggested that minor overall adjustments in size, protein conformation and relative orientation of reaction interfaces have been optimized to provide the ideal environments for electron transfer, proton translocation and generation of adenosine triphosphate (ATP). Additionally, three unique substitution sites were identified under selection in ND6, which could be potentially important adaptive changes contributing to cellular energy production. Our findings suggested that adaptive evolution may occur in alpine pheasants, which are an important complement to the knowledge of genetic mechanisms against the high-altitude environment in non-mammal animals.

Nycticebus pygmaeus has been listed as vulnerable by IUCN due to habitat destruction and hunting for traditional medicine and trade. Identifying the species and sources in markets is important for resource conservation and trade controls. In this study, we sequenced and characterized the complete mitochondrial genome of N. pygmaeus. The entire mtDNA of N. pygmaeus, 16,856 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and one control region, was similar to those of other Nycticebus in gene arrangement and composition. This work contributes to providing basic molecular data which is critical for further genetic research and conservation of this vulnerable species.

In this study, we sequenced the complete mitochondrial genome of the bird Garrulax albogularis. The mitochondrial genome of G. albogularis was 17,870 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two control regions. The overall base composition of the mitogenome was biased toward at 53.83%A + T content. ND6 and nine tRNA genes were encoded on the L-strand. The other protein-coding genes (PCGs) and tRNA genes were all distributed on the H-strand.

The complete mitochondrial genome of Eurasian lynx (Lynx lynx) from China has been described in this study. It has a circular genome of 16,996 bp with a higher A + T content of 58.65%, and the base...

In this study, we first characterized the complete mitogenome of Pygathrix nigripes, and analysed its phylogenetic status. The circular mitogenome was 16,534 bp in length, and contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and one non-coding control region (D-loop). These genes except ND6 and 8 tRNA genes were encoded on the H-strand. The phylogenetic analysis exhibited that our sequence formed a sister branch with P. cinereal and P. nemaeus of genus Pygathrix, which showed a closer genetic relationship of the three species. These information contribute to molecular, phylogenetic studies and genetic diversity conservation for this species.

The red-tail knobby newt (Tylototriton kweichowensis), endemic to Yunnan–GuizhouPlateau (China), is classed as vulnerable amphibian by IUCN. Recently, habitat destructionand degradation are major threats to this species. To assess the genetic diversity andpopulation structure with this species, we determined the sequence of the mitochondrialDNA (mtDNA) control region and tRNA-Phe gene in 13 individuals from two sites inYunnan, and reanalyzed 58 published samples from 12 sties in Yunnan and Guizhou.Nineteen variable sites were observed and 28 haplotypes were identified. Haplotype di-versity was high (0.9364) and nucleotide diversity among all haplotypes was relatively low(0.00219). Bayesian tree and a median-joining network revealed no significant phylo-geographic structure. Both the bell-shaped pairwise mismatch distribution and significantnegative values of Fu’s F S suggested that red-tail knobby newt have experienced a recentpopulation expansion. Base on the results of this study, several conservation recommen-dations on this vulnerable species are discussed.Crown Copyright 2013 Published by Elsevier Ltd. All rights reserved.

We newly sequenced the near complete mitochondrial genome of Polypedates braueri. The total length of the P. braueri partial mitogenome is 13 144 bp, with GenBank accession no. KT921226. It consists of 11 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNA), and 18 transfer RNA genes (tRNA). Most of the genes are encoded on the H-strand, except for seven tRNA and ND6, which are encoded on the L-strand. Our mitogenomic phylogenetic tree shows that the relationships between the genera Rhacophorus and Polypedates were well supported.

We sequenced the complete mitochondrial DNA genome of Yuhina diademata by means of polymerase chain reaction. The circle genome (17 834 bp in length) contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 control regions (Dloop1 and Dloop2), which was similar to the other published mitogenome of Timaliidae species. Most PCGs began with ATG, while COI and ND2 genes started with GTG. Nine of the PCGs used complete (TAA) or incomplete (TA- or T--) stop codon, while ND1 and ND6 genes ended with AGA, COI gene ended with AGG, and ND6 gene with TAG. Overall base composition of the complete mtDNA was 30.30% A, 23.81% T, 31.72% C, and 14.17% G. All the PCGs in Y. diademata were distributed on the H-strand, except for the ND6 gene and eight tRNA genes which were encoded on the L-strand.

In this study, the near complete mitogenome sequence (15,469 bp) of Oreolalax major was determined using polymerase chain reaction (PCR). It includes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes and 19 transfer RNA (tRNA) genes (GenBank accession number KU310894). The features of O. major have one more tRNA gene (tRNAMet) behind the original one before ND2 which is similar to Leptobrachium boringii. Phylogenetic analyses were based on the concatenated sequences of the 13 protein-encoding genes of O. major and other related species.

The complete mitochondrial of Babax lanceolatus is 17 849 bp in length. The contents of A, C, T, and G in the mitochondrial genome were 29.53%, 32.62%, 23.72%, and 14.13%, respectively. The mitogenome of B. lanceolatus were composed of 13 typical protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two putative control regions. All protein-coding, rRNA, and tRNA genes were similar to those of other Passeriformes in gene arrangement and composition. Garrulax perspicillatus was the nearest sister to B. lanceolatus, and they were clustered with other species of Garrulax family. The results could provide essential information for molecular phylogenetic and evolutionary analyses of Passeriformes.