Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Terek sandpiper, Xenus cinereus (Charadriiformes: Scolopacidae).

ABSTRACT: The complete mitochondrial DNA genome of Terek sandpiper, Xenus cinereus, was detected by using polymerase chain reaction method and DNASTAR software package. The circular mitogenome (16,817?bp in length) contains 13 protein-coding genes, 2 rRNA genes (12S ribosomal RNA and 16S ribosomal RNA), 22 tRNA genes and a control region. The content of four kinds of bases of the complete mitochondrial DNA is 30.7% for A, 24.9% for T, 30.2% for C and 14.3% for G, respectively. To validate our data, 12 published complete mitochondrial genomes of Charadriiformes along with the genome of Terek sandpiper were used to construct the phylogenetic tree.

SUBMITTER: Liu W

PROVIDER: S-EPMC7800694 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of Terek sandpiper, Xenus cinereus (Charadriiformes: Scolopacidae).

Liu Wei W Zhang Yi Y Hu Dongfang D Ge Xiaohui X Chen Peng P Chang Qing Q

Mitochondrial DNA. Part B, Resources 20161018 1

The complete mitochondrial DNA genome of Terek sandpiper, Xenus cinereus, was detected by using polymerase chain reaction method and DNASTAR software package. The circular mitogenome (16,817 bp in length) contains 13 protein-coding genes, 2 rRNA genes (12S ribosomal RNA and 16S ribosomal RNA), 22 tRNA genes and a control region. The content of four kinds of bases of the complete mitochondrial DNA is 30.7% for A, 24.9% for T, 30.2% for C and 14.3% for G, respectively. To validate our data, ...[more]

PMID: 33473608

Similar Datasets

Complete mitochondrial genome of Tringa erythropus (Charadriiformes: Scolopacidae).

Project description:The spotted redshank Tringa erythropus is a shorebird in the large bird family Scolopacidae. In this study, we sequenced and characterized its complete mitochondrial genome. The mitogenome is a circular DNA molecule of 16,683 bp in length, containing 13 protein-coding genes, 22 tRNA, 2 rRNA genes, and an AT-rich region. Its gene arrangement pattern is identical with typical bird species. Based on our data combined with the mitgenome DNA sequences of 12 Scolopacidae birds from GenBank, phylogenetic analysis indicated that T. erythropus, Arenaria interpres, and Eurynorhynchus pygmeus formed a group.

| S-EPMC7799656 | biostudies-literature

The complete mitochondrial genome of Tringa ochropus (Charadriiformes, Scolopacidae).

Project description:The green sandpiper Tringa ochropus (Charadriiformes, Scolopacidae) is completely migratory with an extremely large distribution range. However, its habitat ecology, and disease spreading are relatively understudied, and the molecular genetics is relatively unclear. In this study, we report the complete mitochondrial genome of T. ochropus, which is a circular molecule of 16,906?bp in length and the A?+?T content of overall base of the composition of H-strand is 54.88% (A: 31.62%, T: 25.53%, C: 29.47%, G: 13.38%). This study strongly supports the monophyly of Charadriiformes, and division of the order into three major clades, including Lari, Scolopaci, and Charadrii.

| S-EPMC7799479 | biostudies-literature

The complete mitochondrial genome of Calidris tenuirostris (Charadriiformes: Scolopacidae).

Project description:There is a lack of genomic information on Calidris tenuirostris, which can provide valuable resource for genetic diversity and conservation biology. The complete mitogenome of C. tenuirostris was 16,775 bp in length and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and 1 control region (D-loop). The overall nucleotide composition was 31.10% A, 24.9% T, 30.10% C and 13.9% G. The start codon (ATG) and end codon (TAA) were usual. Phylogenomic analysis using mitogenomes supports monophyly of Scolopacidae, and help us understand the evolutionary relationship in charadriiformes.

| S-EPMC7748780 | biostudies-literature

The complete mitochondrial genome of Tringa semipalmata inornata (Charadriiformes; Scolopacidae).

Project description:In this study, we presented the complete mitochondrial genome of Tringa semipalmata. The circular genome is 16,603?bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosome RNA genes and 1 D-loop control regions. The overall nucleotide composition is as follows: 31.2% A, 25.2% T, 29.9% C and 13.6% G, with a total G?+?C content of 43.53%. The phylogenetic tree was constructed to validate the taxonomic status of T. semipalmata, exhibiting it a close relationship to other Tringa species.

| S-EPMC7800691 | biostudies-literature

The complete mitochondrial genome of Marsh Sandpiper Tringa stagnatilis (Charadriiformes, Scolopacidae).

Project description:The complete mitochondrial genome of Marsh Sandpiper Tringa stagnatilis was sequenced in this study. The circular mitogenome was 16,799 bp in length, which contained 13 protein-coding genes, two ribosomal RNAs (12S rRNA and 16S rRNA), 22 transfer RNA genes, and a D-loop region. The overall nucleotide composition was A: 31.51%, T: 25.45%, C: 29.51%, and G: 13.53%. Twenty-eight genes were encoded on the heavy strand, and the remaining nine genes were encoded on the light strand. The common start codon was ATG, and four stop codons and an incomplete stop codon (T-) were used in PCGs. This study improves our understanding of the mitogenomic characteristics and its phylogenetic relationships within Charadriiformes.

| S-EPMC7782464 | biostudies-literature

The complete mitochondrial genome of Eastern Curlew Numenius madagascariensis (Charadriiformes, Scolopacidae).

Project description:The complete mitochondrial genome of Numenius madagascariensis Linnaeus, 1766 was sequenced in this study. The circular mitogenomes was 17,147 bp in length, containing 13 protein-coding genes, two ribosomal RNAs (12S rRNA and 16S rRNA), 22 transfer RNA genes, and a D-loop region. The overall nucleotide composition was A: 31.0%, T: 25.6%, C: 29.5%, and G: 13.9%. Twenty-eight genes were encoded on the heavy strand, while the remaining nine genes were encoded on the light strand. The common start codon was ATG, and three stop codons and an incomplete stop codon (T-) were used in PCGs. This study improves our comprehension of the mitogenomic characteristics and its phylogenetic relationships within Scolopacidae.

| S-EPMC8491663 | biostudies-literature

Complete mitochondrial genome of two shorebirds (Charadriiformes: Scolopacidae), great knot (Calidris tenuirostris) and bar-tailed godwit (Limosa lapponica).

Project description:The mitochondrial genome of Calidris tenuirostris and Limosa lapponica were described using the whole mitochondrial genome obtained from Illumina Next-Generation Sequencing (NGS) technology. Total length of the mitogenome of C. tenuirostris was 16,732bp with slight A+T bias (55.3%). Genome size of L. lapponica was 16,773bp long and A+T biased (56.3%). Both gemones consisting of 2 rRNAs, 13 protein-coding genes, 22 tRNA genes and 1 non-coding regions. This is the first report of complete mitogenomes of these two shorebird species, (C. tenuirostris and of L. lapponica). We observed paraphyletic relationship among the species in the Family Scolopacidae. Also our result showed analogous patterns with the previous studies on the parallel relationships of shorebird species. This study provides basic genetic information for help in understanding phylogenetic relationships . within the Charadriiformes.

| S-EPMC7783118 | biostudies-literature

Complete mitochondrial genome of Haematopus ostralegus (Charadriiformes: Haematopodidae).

Project description:The Eurasian oystercatcher (Haematopus ostralegus), Near Threatened in the IUCN red list, was designated classified endangered species II by the Ministry of Environment of Korea and a Natural Monument (No. 326) by the Cultural Heritage Administration of Korea. In this study, the complete mitochondrial genome (16,798?bp) of H. ostralegus was determined for the first time, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding region. The overall base composition was A (31.4%), C (31.3%), G (13.8%), and T (23.5%), so the percentage of A and T (54.9%) was slightly higher than that of G and C. A phylogenetic analysis using concatenated mitogenomes revealed that the family Haematopodidae has a closer relationship with the family Recurvirostridae and H. ostralegus and H. ater clustered together. The results are expected to provide useful resources for species identification and further phylogenetic studies of genus Haematopus.

| S-EPMC7799934 | biostudies-literature

Complete mitochondrial genome of Aethia cristatella (Charadriiformes: Alcidae).

Project description:The complete mitochondrial genome sequence of the crested auklet, Aethia cristatella, was obtained using high-throughput whole genome sequencing. This is the first report indicating that the complete mitochondrial genome of Aethia has been sequenced. The circular genome is 16,848 bp in length. It contains thirteen protein-coding genes, twenty-two transfer RNAs, two ribosomal RNAs, and a control region. The ND3 gene possessed an insertion mutation. Maximum likelihood phylogenetic analysis demonstrated that A. cristatella is the sister clade of P. aleuticus clustered with the Alcinae species, belonging to Alcidae.

| S-EPMC7720986 | biostudies-literature

Complete mitochondrial genome of the Ruff, Calidris pugnax (Aves, Scolopacidae).

Project description:This paper reports the mitochondrial genome of Calidris pugnax, which is a closed circular molecule of 16,902 bp. The overall base composition of this species is 25.2% T, 30.6% C, 32.0% A, and 12.2% G, with an A + T content of 55.2%. The structure of the mitogenome is a typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis of complete mitochondrial genome concatenated sequences from 13 species from 6 genera was conducted using the maximum-likelihood (ML) model. The topology demonstrated that the mitogenome of this species was genetically closest to that of Calidris tenuirostris. Calidris pugnax mitogenome can contribute to our understanding of the phylogeny and evolution of this species.

| S-EPMC7510813 | biostudies-literature