Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The characteristic of corvus pectoralis's complete mitochondrial genome and phylogeny analysis.

ABSTRACT: The Collared Crow (Corvus pectoralis), in the order Passeriformes, it widely distributed in large areas encompassing China and northern Vietnam. It is a vulnerable bird that is of international concern. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of C. pectoralis. The results showed that the whole genome of C. pectoralis was 16,857 bp long and contains 13 PCGs, 2 ribosomal RNA genes, 23 transfer RNA genes, and 1 loop region. The overall base composition of the mitochondrial DNA was 31.13% for A, 29.52% for C, 24.46% for T, and 14.89% for G, with a GC content of 44.41%. The phylogenetic tree showed that C. pectoralis was clustered with C. brachyrhynchos and then together with other two crows in family Passeriformes. This information will be useful in the current understanding of the phylogeny and evolution of Passeriformes.

SUBMITTER: Huang T

PROVIDER: S-EPMC7707285 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of Daurian jackdaw (Corvus dauuricus).

Project description:In this study, the complete mitochondrial genome of Daurian jackdaw (Corvus dauuricus, Pallas, 1776) was sequenced and deposited to GeneBank for the first time using muscle tissue. This mitochondrial genome is a circular molecule of 16921 bp in length and sequence analysis showed it contains 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and D_loop. The phylogenetic analysis basis of 12 protein-coding genes except for ND6 gene of 13 species shows that most of the genus of Corvus were grouped into two clades, and C. dauuricus was basal to all other Corvus.

| S-EPMC7748756 | biostudies-literature

Sequence and phylogeny of the complete mitochondrial genome of the Himalayan jungle crow (Corvidae: Corvus macrorhynchos intermedius) from Pakistan.

Project description:Corvus macrorhynchos formerly referred to as the jungle crow or the large-billed crow is a polytypic species with unresolved taxonomy, comprising various subspecies widespread across South, Southeast, and East Asia. In this study, we report the complete mitogenome of one of these subspecies, Corvus macrorhynchos intermedius (Himalaya crow), from Pakistan. The mitochondrial genome is circular, 16,927 bp and contains typical animal mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA) and one non-coding region (D-loop) with a nucleotide content of A (30.6%), T (24.8%), G (14.8%), and C (29.8%). Phylogenetic analysis using the whole mitochondrial genome showed that C. m. intermedius and only reported subspecies Corvus macrorhynchos culminatus (Indian Jungle crow) are genetically distinct and it supports the recognition of the latter as a separate biospecies.

| S-EPMC7748637 | biostudies-literature

The first complete mitochondrial genome sequence of an Australian raven (Corvus coronoides).

Project description:Here, we report the complete mitochondrial genome of an Australian raven (Corvus coronoides). The mitogenome of C. coronoides was characterised as a circular molecule of 16,925?bp in length encoding a typically conserved structure similar to those of other Corvidae. It consisted of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, with all protein-coding sequences commencing with methionine. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 980?bp and 1600?bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of C. coronoides was slightly higher AT (56.0%) content than GC (44.0%). A phylogenetic tree using available complete mitogenome sequences of the family Corvidae revealed a close evolutionary relationship of C. coronoides with the now extinct Chatham raven (C. moriorum), a large songbird that was native to the Chatham Islands east of New Zealand.

| S-EPMC7800940 | biostudies-literature

Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius.

Project description:Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.

| S-EPMC1360101 | biostudies-literature

The complete mitochondrial genome of the snakeskin gourami, Trichopodus pectoralis (Regan 1910) (Teleostei: Osphronemidae).

Project description:We sequenced and assembled three whole mitogenome sequences of the commercially important snakeskin gourami Trichopodus pectoralis isolated from Malaysia (introduced), Viet Nam (native) and Thailand (native). The mitogenome length range from 16,397 to 16,420?bp. The final partitioned nucleotide alignment consists of 14,002?bp and supports the monophyly of the genus Trichopodus (95% ultrafast bootstrap support) with T. trichopterus forming a sister group with the members of T. pectoralis.

| S-EPMC7800780 | biostudies-literature

Complete mitochondrial genome of Pelecanus crispus and its phylogeny.

Project description:The Dalmatian Pelican (Pelecanus crispus), in the order Pelecaniformes, its habitat is distributed in Europe, Asia, and Africa. It is a large waterfowl that is of international concern. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of P. crispus. The results showed that the whole genome of P. crispus was 16,131 bp in length, and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and one non-coding control region. The overall base composition of the mitochondrial DNA was 30.48% for A, 23.15% for T, 31.68% for C, and 14.69% for G, with a GC content of 46.37%. A phylogenetic tree of P. crispus in Pelecaniformes confirmed that P. crispus was sister to C. occidentalis. This information will be useful in the current understanding of the phylogeny and evolution of Pelecaniformes.

| S-EPMC7706529 | biostudies-literature

The Complete Mitochondrial Genome of Coptotermes 'suzhouensis' (syn. Coptotermes formosanus) (Isoptera: Rhinotermitidae) and Molecular Phylogeny Analysis.

Project description:Coptotermes suzhouensis (Isoptera: Rhinotermitidae) is a significant subterranean termite pest of wooden structures and is widely distributed in southeastern China. The complete mitochondrial DNA sequence of C. suzhouensis was analyzed in this study. The mitogenome was a circular molecule of 15,764 bp in length, which contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A+T-rich region with a gene arrangement typical of Isoptera mitogenomes. All PCGs were initiated by ATN codons and terminated by complete termination codons (TAA), except COX2, ND5, and Cytb, which ended with an incomplete termination codon T. All tRNAs displayed a typical clover-leaf structure, except for tRNASer(AGN), which did not contain the stem-loop structure in the DHU arm. The A+T content (69.23%) of the A+T-rich region (949 bp) was higher than that of the entire mitogenome (65.60%), and two different sets of repeat units (A+B) were distributed in this region. Comparison of complete mitogenome sequences with those of Coptotermes formosanus indicated that the two taxa have very high genetic similarity. Forty-one representative termite species were used to construct phylogenetic trees by maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogenetic analyses also strongly supported (BPP, MLBP, and MPBP = 100%) that all C. suzhouensis and C. formosanus samples gathered into one clade with genetic distances between 0.000 and 0.002. This study provides molecular evidence for a more robust phylogenetic position of C. suzhouensis and inferrs that C. suzhouensis was the synonymy of C. formosanus.

| S-EPMC5846291 | biostudies-literature

The complete mitochondrial genome of Sarcocheilichthys davidi and its phylogeny.

Project description:Sarcocheilichthys davidi is a small-size ornamental freshwater species. In the present study, the complete mitochondrial genome of S. davidi was first determined using the next-generation sequencing technology. The result showed that the circular mitogenome was 16,675?bp in length, contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and two non-coding regions: origin of light-strand replication (OL) and displacement loop locus (D-loop). In addition to ND6 and eight tRNA genes, most mitochondrial genes were encoded on the heavy strand. Furthermore, the overall base composition was 29.97% A, 26.12% T, 26.86% C, 17.04% G, respectively, and showed AT-rich feature (56.09%). Moreover, phylogenetic analysis based on the tandem 13 PCGs nucleotide sequences indicated that S. davidi had a close relationship with S. snigripinnis and S. variegatus wakiyae. The complete mitogenome sequence of S. davidi would contribute to the better understanding of molecular systematics, selection, conservation, species identification and evolution of this species.

| S-EPMC7799733 | biostudies-literature

The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny.

Project description:To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.

| S-EPMC3313511 | biostudies-literature

Complete mitochondrial genome of the snakehead (Channa gachua) and its phylogeny.

Project description:In present study, the mitochondrial genome (mitogenome) of Channa gachua was determined and the phylogenetic relationship of Channidae fish was reconsidered. The mitogenome of the C. gachua is 16547?bp in length, containing 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosome RNA genes (rRNAs), a control region (D-loop) and an origin region of replication on the light-strand (OL). The overall nucleotide composition is 28.32% A, 26.58% T, 29.41% C, 15.69% G, with 54.90% AT, respectively. Phylogenetic analyses revealed that C. gachua belongs to the genus Channa and shares a close relationship with C. marulius and C. striata.

| S-EPMC7707787 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data