Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome sequence of tufted deer (Elaphodus cephalophus) with phylogenetic analysis.

ABSTRACT: 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.

SUBMITTER: Zhang L

PROVIDER: S-EPMC7707186 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete mitochondrial genome sequence of tufted deer (Elaphodus cephalophus) with phylogenetic analysis.

Zhang Lin L Yao Yongfang Y Li Diyan D Wu Jiayun J Wen Anxiang A Xie Meng M Wang Qin Q Zhu Guangxiang G Ni Qingyong Q Zhang Mingwang M Xu Huailiang H

Mitochondrial DNA. Part B, Resources 20191025 2

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 ...[more]

PMID: 33366187

Similar Datasets

Molecular identification and mitogenome character of illegally traded tufted deer, Elaphodus cephalophus cephalophus.

Project description:The total mitogenome of the confiscated material of tufted deer, Elaphodus cephalophus cephalophus was sequenced and annotated. It is 16,351bp in length and contained 2 ribosomal RNAs, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs) and, 1 control region (CR). Phylogenetic analyses showed the close relationship of Elaphodus and Muntiacus, and monophyletic clades of genera Elaphodus and Muntiacus.

| S-EPMC7782236 | biostudies-literature

Identification and characterization of a novel bocaparvovirus in tufted deer (Elaphodus cephalophus) in China.

Project description:We used viral metagenomics and next-generation sequencing to identify a novel strain of bocaparvovirus in the intestinal tract of tufted deer (Elaphodus cephalophus), tentatively named "Elaphodus cephalophus bocaparvovirus" (ECBOV). A nearly complete genome sequence of 5,354 nucleotides was obtained, which had the typical genome organization and protein motifs of a bocaparvovirus. Sequence comparisons and phylogenetic analysis revealed that ECBOV may be a new ungulate bocaparvovirus. The identification and characterization of viruses in wildlife will facilitate our understanding of genetic evolution and cross-species transmission and thus further reduce the potential threat to human and animal health.

| S-EPMC8590863 | biostudies-literature

The complete mitochondrial genome of Siberian roe deer (Capreolus pygargus bedfordi) and its phylogenetic analysis.

Project description: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.

| S-EPMC7748484 | biostudies-literature

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia.

Project description:Plant mitochondrial genomes (mitogenomes) are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitogenome of any species in the genus of Photinia has been reported. In this study, using NGS sequencing, we reported the mitogenome assembly and annotation of Photinia serratifolia, which is 473,579 bp in length, contains 38 protein-coding genes, 23 tRNAs, and 6 rRNAs, with 61 genes have no introns. The rps2 and rps11 genes are missing in the P. serratifolia mitogenome. Although there are more editing sites (488) in the P. serratifolia mitogenome than in most angiosperms, fewer editing types were found in the P. serratifolia mitogenome, showing a clear bias in RNA-editing. Phylogenetic analysis based on the mitogenomes of P. serratifolia and 8 other taxa of the Rosaceae family reflected the exact evolutionary and taxonomic status of P. serratifolia. However, Ka/Ks analysis revealed that 72.69% of the protein-coding genes in the P. serratifolia mitogenome had undergone negative selections, reflecting the importance of those genes in the P. serratifolia mitogenome. Collectively, these results will provide valuable information for the evolution of P. serratifolia and provide insight into the evolutionary relationships within Photinia and the Rosaceae family.

| S-EPMC9840629 | biostudies-literature

The complete mitochondrial genome sequence and phylogenetic analysis of Squalidus multimaculatus.

Project description:This study reports the complete mitochondrial genome of Squalidus multimaculatus. The length of the mitochondrial genome of S. multimaculatus is 16,597 bp, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The overall base composition of A, G, T, and C is 28%, 18.8%, 25%, and 28.2%, respectively. A phylogenetic analysis by the neighbour-joining method showed a close relationship between S. multimaculatus and S. japonicus coreanus. We believe these results will provide essential data for phylogeographic studies of the genus Squalidus.

| S-EPMC7781996 | biostudies-literature

Complete mitochondrial genome sequence and phylogenetic analysis of Lycodes polaris (Sabine, 1824).

Project description:Lycodes polaris is one of the most widely distributed and abundant eelpout species on the Arctic continental shelves with full mitogenome information unavailable. In this paper, complete mitochondrial genome of L. Polaris was determined with 16,595 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding regions (origin of light strand replication and control region). All the protein-coding genes choose ATG as start codon in addition to that COI using GTG. Most genes use TAA or TAG as the stop codon while three others ended with incomplete stop codons. Phylogenetic relationship of L. polaris was also reconstructed. Our result will provide important basis for further studies of L. polaris.

| S-EPMC7687599 | biostudies-literature

Complete mitochondrial genome sequence and phylogenetic analysis of Arion ater (Stylommatophora: Arionidae).

Project description:Arion ater are a group of mollusks, almost all of which live in a dark and humid environment during their life cycle. In this study, the complete mitogenome of Arion ater was sequenced using next generation sequencing, analyzed and compared with other Stylommatophorans. The total length of the mitochondrial genome is 14,314 bp and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The genome has a typical mitochondrial gene sequence of Arion. Phylogenetic analysis of the mitochondrial genomes of 27 species of Stylommatophora showed that the Arion ater, Arion rufus and Arion vulgaris forms a monophyletic group with other species.

| S-EPMC8439229 | biostudies-literature

Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study.

Project description:Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.

| S-EPMC5103815 | biostudies-literature

The complete mitochondrial genome sequence of Triplophysa stenura (Teleostei, Cypriniformes): genome characterization and phylogenetic analysis.

Project description:The nemacheilid genus Triplophysa is widely distributed in the Qinghai-Tibet Plateau and its adjacent areas. The complete mitochondrial genome of the loach Triplophysa stenura collected from the Peigucuo Lake was sequenced. The genome was 16,569 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region (D-loop). Most of the genes were encoded on the heavy strand, except for ND6 and eight tRNA genes. The overall base composition of T. stenura was 27.8% for A, 28.4% for T, 25.4% for C, 18.4% for G, with a slight A + T rich feature (56.2%). Phylogenetic analyses showed that all Triplophysa species clustered together and T. stenura formed a sister relationship with T. tibetana. The complete mitogenome data of T. stenura would provide essential information in understanding phylogenetic relationships among Triplophysa species.

| S-EPMC7800979 | biostudies-literature

Characterization of the complete mitochondrial genome sequence of Charybdis bimaculata and phylogenetic analysis.

Project description:In this study, the complete mitogenome of Charybdis bimaculata was sequenced and annotated. The mitogenome is 15,441?bp in length, containing 37 classical eukaryotic mitochondrial regions (13 typical protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes) and a non-coding control region. Most of the genes are initiated with ATA, ATG, and ATT, though GTG is also used as an initiation codon. Twelve PCGs stop with complete termination codon TAA and TAG, while Cob uses incomplete codon (T-). The phylogenetic relationships based on 13 PCGs show that C. bimaculata clusters closest to C. fariata and C. natator.

| S-EPMC7799625 | biostudies-literature