Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC9621200 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Zhao Yao Y Meng Dehuai D Si Yuhui Y Zhou Xiaoyu X Teng Liwei L Liu Zhensheng Z

Mitochondrial DNA. Part B, Resources 20221027 10

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 ...[more]

PMID: 36325286

Similar Datasets

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

Project description: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.

| S-EPMC7707216 | biostudies-literature

Complete mitochondrial genome of yellow-rumped honeyguide Indicator xanthonotus (Piciformes: Indicatoridae).

Project description:In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of Indicator xanthonotus. The whole genome of I. xanthonotus was 17,603 bp in length and contained 14 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and two non-coding control regions. The overall base composition of the mitochondrial DNA was 31.09% for A, 27.34% for T, 28.96% for C, and 12.61% for G, with a GC content of 41.57%. A phylogenetic tree strongly supported that I. xanthonotus clustered with another Piciformes species by high probability.

| S-EPMC7800801 | biostudies-literature

Low level of extra-pair paternity between nearest neighbors results from female preference for high-quality males in the yellow-rumped flycatcher (Ficedula zanthopygia).

Project description:Extra-pair copulation is considered to be a means by which females can modify their initial mate choice, and females might obtain indirect benefits to offspring fitness by engaging in this behavior. Here, we examined the patterns of extra-pair paternity and female preferences in the yellow-rumped flycatcher (Ficedula zanthopygia). We found that female yellow-rumped flycatchers are more likely to choose larger and relatively highly heterozygous males than their social mates as extra-pair mates, that the genetic similarity of pairs that produced mixed-paternity offspring did not differ from the similarity of pairs producing only within-pair offspring, and that extra-pair offspring were more heterozygous than their half-siblings. These findings support the good genes hypothesis but do not exclude the compatibility hypothesis. Most female yellow-rumped flycatchers attained extra-pair paternity with distant males rather than their nearest accessible neighboring males, and no differences in genetic and phenotypic characteristics were detected between cuckolded males and their nearest neighbors. There was no evidence that extra-pair mating by female flycatchers reduced inbreeding. Moreover, breeding density, breeding synchrony and their interaction did not affect the occurrence of extra-pair paternity in this species. Our results suggest that the variation in extra-pair paternity distribution between nearest neighbors in some passerine species might result from female preference for highly heterozygous males.

| S-EPMC5336208 | 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

Characterization of the complete mitochondrial genome of band-rumped Storm-petrel, Hydrobates castro.

Project description:In this study, the complete mitochondrial genome of band-rumped Storm-petrel, Hydrobates castro, was determined through sequencing of PCR fragments. The complete mitochondrial genome of H. castro was 17,065 bp in length and encoded 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes. The overall nucleotide composition is: 30.4% A, 24.5% T, 30.9% C, and 14.2% G, with a total G + C content of 45.1%. By phylogenetic analysis using Bayes method, H. castro showed the closest relationship with the white-faced storm petrel (Pelagodroma marina).

| S-EPMC7799991 | biostudies-literature

The complete mitochondrial genome of Gobio huanghensis (Cypriniformes: Cyprinidae) in the Yellow River, China.

Project description:Gobio huanghensis, a member of the eponymous genus within the Cyprinidae, family of the Cypriniformes order, is an endemic fish species found exclusively in the upper reaches of the Yellow River, spanning from Yinchuan to Lanzhou. This study presents the first comprehensive report of the complete mitochondrial genome sequence of G. huanghensis, encompassing 16,604 base pairs (bp) with a nucleotide composition of 26.3% cytosine (C), 17.6% guanine (G), 29.4% adenine (A), and 26.7% thymine (T). In congruence with other species in the Gobio genus, its mitochondrial genome comprises 37 genes, including two ribosomal RNA genes, 13 protein-coding genes (PCGs), and 22 transfer RNA genes. Notably, COX1 initiates with the start codon GTG, distinct from the typical ATG start codon of other PCGs. The mitogenome exhibits four types of stop codons: TAA, TAG, TA-, and T--. Phylogenetic analyses, grounded in complete mitochondrial sequences, position G. huanghensis at the forefront of one of two major clusters within the genus Gobio, corroborating existing morphological classifications. These findings offer valuable theoretical insights for the taxonomic classification, conservation, and population genetics of G. huanghensis.

| S-EPMC10885765 | biostudies-literature

Complete mitochondrial genome of yellow meal worm (Tenebrio molitor).

Project description:The yellow meal worm (Tenebrio molitor L.) is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. molitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A+T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were the same as the most common type suggested as ancestral for insects. Two protein-coding genes used atypical start codons (CTA in ND2 and AAT in COX1), and the remaining 11 protein-coding genes started with a typical insect initiation codon ATN. All tRNAs showed standard clover-leaf structure, except for tRNA(Ser) (AGN), which lacked a dihydrouridine (DHU) arm. The newly added T. molitor mitogenome could provide information for future studies on yellow meal worm.

| S-EPMC4790282 | biostudies-literature

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences.

Project description:Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences from 287 Ficedula flycatchers representing four species, with the objectives of evaluating the causes of genome-wide variation in the abundance of ROH and inferring historical demography. ROH were clearly more abundant in genomic regions with low recombination rate. However, this pattern was substantially weaker when ROH were mapped using genetic rather than physical single nucleotide polymorphism (SNP) coordinates in the genome. Empirical results and simulations suggest that high ROH abundance in regions of low recombination was partly caused by increased power to detect the very long IBD segments typical of regions with a low recombination rate. Simulations also showed that hard selective sweeps (but not soft sweeps or background selection) likely contributed to variation in the abundance of ROH across the genome. Comparisons of the abundance of ROH among several study populations indicated that the Spanish pied flycatcher population had the smallest historical effective population size (Ne) for this species, and that a putatively recently founded island (Baltic) population had the smallest historical Ne among the collared flycatchers. Analysis of pairwise IBD in Baltic collared flycatchers indicated that this population was founded <60 generations ago. This study provides a rare genomic glimpse into demographic history and the mechanisms underlying the genome-wide distribution of ROH.

| S-EPMC5340341 | biostudies-literature

Complete mitochondrial genome of Ulva prolifera, the dominant species of green macroalgal blooms in Yellow Sea, China.

Project description:Ulva prolifera (U. prolifera), a green macroalgae, is widely known as the dominant species of the world's largest macroalgal blooms in the Yellow Sea, China. In this study, we sequenced and annotated the complete mitochondrial genome of U. prolifera (GenBank accession number: KU161104). The genome consists of circular chromosomes of 61 962 bp and encodes a total of 26 protein-coding genes include nine ribosomal protein genes, five atp genes, three cox genes, eight nad genes and cob gene. Phylogenetic analysis showed U. prolifera clustered into Ulvo phyceae clade and had close genetic relationship with algae Ulva fasciata.

| S-EPMC7799800 | biostudies-literature

The complete mitochondrial genome of Eastern Yellow Wagtail (Motacilla tschutschensis).

Project description:Motacilla tschutschensis is a species of small passerine bird belonging to the family Motacillidae. Complete mitochondrial genome of Eastern Yellow Wagtail (M. tschutschensis) has been sequenced in this study. The genome is 16,829 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22 tRNA genes. The phylogenetic tree was reconstructed using the Bayesian analysis method, indicating that M. tschutschensis was closely related to Motacillalugens and Motacillaalba.

| S-EPMC7707198 | biostudies-literature