Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of red-throated flycatcher Ficedula albicilla (Passeriformes: Ficedula).

ABSTRACT: We report the mitochondrial genome of Ficedula albicilla. The overall base composition of F. albicilla mitogenome is 29.49%A, 15.06%G, 32.98%C, and 22.47%T, with an A + T content of 51.96%. The total length of the sequence is 16,791 bp (13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control regions). Phylogenetic analysis was performed based on the concatenated nucleotide sequences of cytochrome c oxidase subunit I and cytochrome b using the neighbor-joining method and the Kimura 2-parameter model in MEGA 7.0 with 1000 bootstrap replicates.

SUBMITTER: Zhang XR

PROVIDER: S-EPMC7707216 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of the Yellow-rumped Flycatcher (Ficedula zanthopygia) from Maorshan, China.

Project description:The Yellow-rumped Flycatcher (Ficedula zanthopygia) is a secondary cavity nesting bird and widely distributed in China, Mongolia, Russia and Korea. In this study firstly sequenced the mitotic genome of the Yellow-rumped Flycatcher (Ficedula zanthopygia) gathered at Maorshan, China, using Illumina high-throughput sequencing technology, and then annotated the assembly. The total length of the complete mitochondrial genome is 16,730 bp and it consists of 13 protein-coding, 22 tRNA, 2 rRNA genes, and 1 control region (CR). The CR is 1148 bp in length. The nucleotide composition is 29.59% A, 14.75% T, 32.13% G, 23.54% C. The result of phylogenetic analysis showed that there is close genetic relationship among Ficedula zanthopygia and Ficedula hyperythra.

| S-EPMC9621200 | biostudies-literature

Complete mitochondrial genome of white-throated rock-thrush Monticola cinclorhynchus gularis (Passeriformes: muscicapidae).

Project description:The white-throated rock-thrush Monticola cinclorhynchus gularis is a subspecies bird in the family Muscicapidae of the order Passeriformes, which is distributed in Southeast Siberia to Northeast China and Korea, winters to Southeast Asia. In this study, we determined its complete mitochondrial genome (mtDNA) by the PCR-based method. The complete mtDNA is a 16,801 bp circular molecule containing 37 typical genes. The gene order is identical with the standard avian gene order. All protein-coding genes start with a typical ATG codon except for COI. The termination codon is usually the standard TAA. The 12S rRNA is 984 bp, and the 16S rRNA is 1602 bp in length. All tRNAs possess the classic clover leaf secondary structure except for tRNASer (AGN) and tRNACys (CUN), which lack the 'DHU' stem, only forming a simple loop. The non-coding regions contain a 1222 bp long control region (D-loop) and a few intergenic spacers. The phylogenetic tree based on some mitogenomes from Muscicapidae and Turdidae indicates that M. cinclorhynchus gularis and Phoenicurus auroreus are in the same branch in the group Muscicapidae.

| S-EPMC7875201 | biostudies-literature

Ficedula albicilla

Project description:Ficedula albicilla

| PRJNA959120 | ENA

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 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

Inferring the demographic history of European Ficedula flycatcher populations.

Project description:BackgroundInference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher.ResultsWe applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations.ConclusionsOur results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.

| S-EPMC3556140 | 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

The complete mitochondrial genome of Turdus obscurus (Passeriformes: Turdidae).

Project description:The Eyebrowed Thrush (Turdus obscurus) is a highly migratory bird, which breeds in northeastern Asia and overwinters in southeastern Asia. We obtained the mitochondrial genome of T. obscurus by Sanger sequencing. The mitogenome was 16,739 bp in length, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. Its composition is consistent with the species in genus Turdus. Phylogenetic analysis based on the whole mitochondrial genome showed that the relationship between T. obscurus and Turdus kessleri was relatively close. This study improves the understanding of phylogeny and genetics of Turdidae and Muscicapoidea.

| S-EPMC8477923 | 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