Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala - characterization and phylogenetic analysis.

ABSTRACT: Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species and scientific basis for phylogenetic revision of the genus Psittacula.

SUBMITTER: Dey P

PROVIDER: S-EPMC8034733 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The first complete mitochondrial genome of Blossom-headed Parakeet Psittacula roseata (Psittaciformes: Psittacidae).

Project description:Blossom-headed Parakeet Psittacula roseate is listed as Near Threatened on the IUCN Red List of Threatened Species because of its habitat loss, and declining population. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of P. roseata. The whole genome of P. roseata was 16,814 bp in length, and contained 14 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control regions. The overall base composition of the mitochondrial DNA was 31.88% for A, 22.00% for T, 32.88% for C, 13.23% for G, with a GC content of 46.11%. A phylogenetic tree strongly supported that genus Psittacula closely related with genus Eclectus by highly probability.

| S-EPMC7782874 | biostudies-literature

Sequence and phylogenetic analysis of the mitochondrial genome for red-breasted parakeet Psittacula alexandri (Psittaciformes: Psittacidae).

Project description:In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of Psittacula alexandri. The whole genome of P. alexandri was 16,883 bp in length, and contained 14 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control regions. The overall base composition of the mitochondrial DNA was 30.87% for A, 22.36% for T, 32.82% for C, and 13.95% for G, with a GC content of 46.77%. A phylogenetic tree strongly supported that P. alexandri closely related with Eclectus roratus by highly probability.

| S-EPMC7707433 | biostudies-literature

The first complete mitogenome of Indian ringneck (Psittacula krameri) demonstrates close phylogenetic relationship with Eclectus parrot.

Project description:This study was aimed to sequence the first complete mitochondrial genome from an Indian ringneck parrot (Psittacula krameri). The mitogenome sequence was circular and 16,413 bp in length. In comparison to other available mitogenome sequences belonging to Psittacidae species, this mitogenome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 21 tRNA genes and a control region; however, this mitogenome missing a tRNA-Glu. The lengths of 12S and 16S ribosomal RNA were 975 bp and 1582 bp, respectively. The overall base composition of the mitogenome of P. krameri was dominated by higher AT (53.5%) than GC (46.5%) content. The complete mitogenome sequence determined in this study would be useful to track the more profound evolutionary history and the conservation of P. krameri.

| S-EPMC7707189 | biostudies-literature

Characterization and phylogenetic analysis of the complete Green-winged macaw (Ara chloropterus) mitogenome.

Project description:In this study, we sequenced and characterized the complete mitochondrial genome of Green-winged macaw (Ara chloropterus) listed on CITES Appendix II. The circular double-stranded genome was 16,991 bp in size and included 22 transfer RNA (tRNA) genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnL and rrnS), and one non-coding control region (D-loop). Both order and arrangement of genes were identical to those of other animal mitogenomes. The base content was 30.00% A, 14.38% G, 23.27% T, and 32.35% C, with an A + T content of 53.37%. Furthermore, phylogenetic analysis indicated that A. chloropterus is closely related to the Blue and yellow macaw (A. ararauna).

| S-EPMC7748460 | biostudies-literature

Complete mitochondrial genome of Parupeneus barberinus (Perciformes, Mullidae): mitogenome characterization and phylogenetic analysis.

Project description:Parupeneus barberinus is a tropical/subtropical reef-dwelling marine fish belonging to the family Mullidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of P. barberinus. The complete mitochondrial genome is 16,560 bp long and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 18 species showed that P. barberinus is clustered with P. multifasciatus and P. chrysopleuron and rooted with other Mullidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.

| S-EPMC7800887 | biostudies-literature

The Nothoaspis amazoniensis Complete Mitogenome: A Comparative and Phylogenetic Analysis.

Project description:The molecular biology era, together with morphology, molecular phylogenetics, bioinformatics, and high-throughput sequencing technologies, improved the taxonomic identification of Argasidae family members, especially when considering specimens at different development stages, which remains a great difficulty for acarologists. These tools could provide important data and insights on the history and evolutionary relationships of argasids. To better understand these relationships, we sequenced and assembled the first complete mitochondrial genome of Nothoaspis amazoniensis. We used phylogenomics to identify the evolutionary history of this species of tick, comparing the data obtained with 26 complete mitochondrial sequences available in biological databases. The results demonstrated the absence of genetic rearrangements, high similarity and identity, and a close organizational link between the mitogenomes of N. amazoniensis and other argasids analyzed. In addition, the mitogenome had a monophyletic cladistic taxonomic arrangement, encompassed by representatives of the Afrotropical and Neotropical regions, with specific parasitism in bats, which may be indicative of an evolutionary process of cospeciation between vectors and the host.

| S-EPMC6024882 | biostudies-literature

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin.

Project description:Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemoglobins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 A resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 A, beta = 109.35 degrees . Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

| S-EPMC2765893 | biostudies-literature

The complete mitogenome of Metopograpsus quadridentatus and phylogenetic analysis.

Project description:The complete mitochondrial genome of Metopograpsus quadridentatus was determined to be 15,520 bp in length. It consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a control region. There are 13 overlapping regions in the genome with 1 to 25 bp length. The largest overlapping region is located between nad1 and trnL1. The AT-skew and GC-skew for the whole mitogenome are both negative, indicating a higher occurrence of Ts than As and Cs than Gs. The molecular data here we presented could play a useful role to study the evolutionary relationships and population genetics of Grapsidae crabs.

| S-EPMC7800309 | biostudies-literature

Complete mitochondrial genome of Echinophylliaaspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning.

Project description:Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coral Echinophylliaaspera (Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows that E.aspera clustered closely with Sclerophylliamaxima (Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome of E.aspera provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.

| S-EPMC6218560 | biostudies-literature

The complete mitogenome of Gracilaria chouae and its phylogenetic analysis.

Project description:Gracilaria chouae, a marine red macroalgae, is a rich source of active substances and is listed as biological and health food material with high economic value. The mitogenome sequence of G. chouae is 25,829?bp. A total of 50 genes were determined, including 24 protein-encoding genes, two rRNA genes, 23 tRNA genes, and one unidentified open reading frame (ORF). Phylogenetic analysis showed that G. chouae clustered together with Gracilariopsis chorda, Gracilariopsis lemanaeformis, Gracilariopsis andersonii, Gracilariophila oryzoides, and Gracilariopsis heteroclada. The mitogenome analysis will help the understanding of Gracilaria evolution.

| S-EPMC7706786 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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