Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of the spotted nutcracker Nucifraga caryocatactes (Passeriformes: Corvidae) from Shan'xi Province, China.

ABSTRACT: We determined the whole mtDNA genome of the Spotted Nutcracker (Nucifraga caryocatactes) in Tianlong Mountain, Shan'xi Province, China. The complete mitochondrial genome is 16,914 bp in length and consists of 13 protein-coding genes (PCGS), 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loops). The nucleotide composition is 25.08% A, 25.08% T, 24.75% G, and 25.08% C. The result of phylogenetic analysis showed that there was close genetic relationship between N. caryocatactes and N. columbiana. It is expected that the complete mitochondrial genome presented here will contribute to the analysis of species distribution.

SUBMITTER: Meng D

PROVIDER: S-EPMC7782841 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete mitochondrial genome of Urocissa erythroryncha (Passeriformes: Corvidae).

Project description:The complete mitochondrial genome of Urocissa erythroryncha is 16930?bp in length. It was predicted to contain 13 PCGs, 22 tRNA genes, and 2 rRNA genes, and a putative control region. All of the PCGs initiated with ATG, except for MT-COX1 which began with GTG and MT-ND3 began with ATA, while stopped by three types of stop codons. Phylogenetic analysis showed that Urocissa erythroryncha and the other species of Corvidae were monophyletic group in this study. And the monophyly of the genus Pyrrhocorax was strongly supported. Moreover, our results also support a sister-group relationship between Corvidae and Muscicapidae.

| S-EPMC7800095 | biostudies-literature

Complete mitochondrial genome sequence for the Taiwan Blue Magpie Urocissa caerulea (Passeriformes: Corvidae).

Project description:Taiwan Blue Magpie (Urocissa caerulea) is endemic to Taiwan and listed as threatened species protected by law. In this study, we first determined and described the complete mitochondrial genome of Taiwan Blue Magpie. The circle genome is 16,928 bp in length, and contains 13 protein coding, 22 tRNA, two rRNA genes, and one non-coding control region (CR). The overall base composition of the mitochondrial DNA is 30.99% for A, 24.69% for T, 30.07% for C, and 14.25% for G. The percentage of G + C content is 44.32%. This work provides fundamental molecular data which will be useful for evolution and phylogeny studies on Corvidae in the future.

| S-EPMC7799675 | biostudies-literature

The complete mitochondrial genome of the Sitta villosa (Passeriformes: Sittidae) from China.

Project description:We describe the whole mtDNA genome of the Chinese nuthatch Sitta villosa in Tianlong Mountain, Shanxi, China. It is actually a circular molecular of 16,816 bp in length and consists 13 protein-coding genes, 22 transfer-RNA genes, 2 ribosomal-RNA genes, and 1 control region (D-loop, 1,243 bp in length). The nucleotide composition is 30.3% A, 30.1% C, 14.5% G, 25.1% T. The phylogenetic analysis based on the maximum likelihood method revealed the relationship of S. villosa was close to the three reported species within the same genus Sitta, which are S. nagaensis, S. himalayensis and S. carolinensis.

| S-EPMC7782314 | biostudies-literature

Complete mitochondrial genome of Grey Treepie, Dendrocitta formosae (Aves: Corvidae).

Project description:We report the complete mitochondrial genome of Dendrocitta formosae. The genome is a closed circular molecule of 16,875 bp, with all genes exhibiting typical avian gene arrangement. The overall base composition of this species' mitogenome is 24.33% T, 30.49% C, 30.17% A, and 15.01% G. The A + T content is 54.50%. Phylogenetic analysis of the complete mitogenome of 12 species conducted using the neighbour-joining method and kimura 2-parameter model suggested that the mitogenome of D. formosae was the closest to that of Pyrrhocorax graculus and P. pyrrhocorax. The results could aid future studies on Dendrocitta and Pyrrhocorax molecular evolution and phylogeny.

| S-EPMC7687445 | biostudies-literature

Complete mitochondrial genome of Sporophila maximiliani (Ave, Passeriformes).

Project description:Sporophila maximiliani, commonly known as Great-billed Seed-Finch or 'bicudo', is a trafficked bird in Brazil due to the species' beauty and singing, which is appreciated by breeders and collectors. Generally, the Environmental Military Police and IBAMA maintain enforcement actions, rescue work, and seizure of illegally traded of 'bicudo' specimens. The genomic DNA of one specimen was sequenced on MiSeq (Illumina) sequencer. The reads obtained were analyzed, trimmed, and de novo assembled using CLC Workbench® v9.0 (CLC Bio-Qiagen). The mitochondrial genome of S. maximiliani consisted of 16,765 base pairs, 2 ribosomal RNA, 22 transporter RNA, 13 protein-coding genes, and 1 control region. The molecular phylogeny demonstrated that the mitochondrial genome of S. maximiliani diverged from others related Passeriformes.

| S-EPMC7800134 | biostudies-literature

Complete mitochondrial genome of Minla ignotincta (Passeriformes: Timaliidae).

Project description:We sequenced the complete mitochondrial genome from Minla ignotincta. The genome sequence was 17 868 bp in length, and the gene arrangement and contents were identical to those of previously reported Timaliidae mitochondrial genomes. The overall base composition of the mitogenome is biased toward A + T content at 54.04%. All protein-coding genes (PCGs) began with ATG. Nine of the 13 PCGs used complete (TAA) or incomplete (TA or T) stop codon, while ND1 and ND5 ended with AGA, COI ended with AGG and ND6 with TAG. All the genes in M. ignotincta were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

| S-EPMC7799491 | biostudies-literature

Population-Wide Failure to Breed in the Clark's Nutcracker (Nucifraga columbiana).

Project description:In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark's nutcrackers (Nucifraga Columbiana) in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark's nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis) cone crops the previous autumn (? an average of 8 ± 2 cones per tree versus ? an average of 20 ± 2 cones per tree during breeding years) and high snowpack in early spring (? 61.2 ± 5.5 cm versus ? 51.9 ± 4.4 cm during breeding years). The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1), a nonbreeding year, as compared to 2012 (6.2 ± 2.0), a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark's nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark's nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences.

| S-EPMC4430254 | biostudies-literature

The complete mitochondrial genome of the Brambling Fringilla montifringilla (Passeriformes: Fringillidae) from Maor Mountain, China.

Project description:The Brambling (Fringilla montifringilla) (Linnaeus 1758) is a member of the Passeriformes family of birds and primarily feeds on grass seeds and grains. Muscle tissue was collected from birds sampled from Moar Mountain, China, and the complete mitochondrial genome was sequenced. Its mitochondrial genome consists of 13 protein-coding genes (PCGs), 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and 1 control region (CR). The genome comprises 30.30% A, 23.32% T, 14.31% G, and 32.07% C bases. Phylogenetically, F. montifringilla is closely related to the Fringilla coelebs, Fringilla teydea teydea and Fringilla polatzeki.

| S-EPMC9815251 | biostudies-literature

The complete mitochondrial genome of Phoenicurus frontalis (Passeriformes: Muscicapidae).

Project description:The Blue-fronted Redstart Phoenicurus frontalis (Muscicapidae) belongs to the family Muscicapidae, distributed in central China, Qinghai-Tibet plateau and the Himalayas. The conservation status of this species is Least Concern (LC) in IUCN. In this study, the complete mitogenome of P. frontalis was determined. The mitogenome is a circular molecule of 16,776 bp in length, containing 13 protein-coding genes, 2 ribosome RNA genes, 22 transfer RNA genes, and 1 non-coding region. We reconstructed a phylogenetic tree based on Bayesian inference for 15 Passeriformes species. The new mitogenome data would provide useful information for application in conservation genetics and further clarify the phylogenetic evolution of this species.

| S-EPMC7782104 | biostudies-literature

The complete mitochondrial genome of Hypsipetes amaurotis (Passeriformes: Pycnonotidae).

Project description:The brown-eared bulbul (Hypsipetes amaurotis) is a medium-sized songbird native to East Asia and characterized by its prominent reddish-brown ear-coverts. Previous studies on it have primarily been from the taxonomic and morphological aspects, with limited research in the realm of molecular biology. In this study, we sequenced and annotated the complete mitochondrial genome of H. amaurotis, which was the first reported complete mitogenome of the genus Hypsipetes. The mitogenome of H. amaurotis is 17,871 bp in length and was predicted to encode 37 typical mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs). Specifically, this mitogenome contains two D-loop control regions that are of similar length and sequencing pattern. A total of 8 Pycnonotidae and six outgroup taxa were used to determine the phylogenetic placement with two methods: Maximum Likelihood Approximation (IQ-TREE) and Bayesian inference (MrBayes). Our findings reveal that H. amaurotis is phylogenetically closely related to Ixos mcclellandii. The outcomes are generally consistent with the phylogenetic trees constructed in previous studies. The data gathered from this research provides valuable insights for future genomic investigations into the evolution, ecology, and conservation of this species.

| S-EPMC11011232 | 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