Browse
Submit Data
Databases
API
Help

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitogenome of Qingyuan chicken (Gallus gallus) by next-generation sequencing and phylogenetic analysis.

ABSTRACT: In this study, the complete mitochondrial genome sequence of the Qingyuan chicken (Gallus gallus) was reported for the first time by using the high-throughput sequencing technology. The complete mitogenome sequence of Qingyuan chicken exhibits a typical genetic structure of vertebrate double-strands circular genome, containing a D-loop region, 2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes. Our work provides a source of useful data for mitochondrial researches and chicken phylogenetic studies.

SUBMITTER: Gu J

PROVIDER: S-EPMC7783063 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitogenome of Qingyuan chicken (Gallus gallus) by next-generation sequencing and phylogenetic analysis.

Gu Jingjing J Li Sheng S

Mitochondrial DNA. Part B, Resources 20200720 3

In this study, the complete mitochondrial genome sequence of the Qingyuan chicken (Gallus gallus) was reported for the first time by using the high-throughput sequencing technology. The complete mitogenome sequence of Qingyuan chicken exhibits a typical genetic structure of vertebrate double-strands circular genome, containing a D-loop region, 2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes. Our work provides a source of useful data for mitochondrial researches and chick ...[more]

PMID: 33458001

Similar Datasets

Next-generation sequencing yields the complete mitogenome of Niya chicken (Gallus gallus).

Project description:In this study, the complete mitochondrial genome sequence of Niya chicken (Gallus gallus) was obtained by using the next-generation sequencing technology for the first time. The complete mitogenome sequence of Niya chicken is 16,784 bp in length, containing 2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNA genes and a D-loop region. Our work provides a valuable source of data for phylogenetic studies and helps us to understand the maternal origins of the native chickens.

| S-EPMC7782777 | biostudies-literature

Next-generation sequencing of the complete mitochondrial genome of the Nixi chicken (Gallus gallus).

Project description:Nixi chicken is a type of Tibetan chickens who lives at high altitudes in China. In this study, we reported the first complete mitochondrial genome of Nixi chicken by using a next-generation sequencing method. The assembled complete mitogenome contains one control region, 2 ribosomal RNAs, 13 protein-coding genes and 22 transfer RNA genes. Our work provides a valuable source of data for the study of the evolution of the Gallus gallus mitochondrial genome and contributes to the Nixi chicken breeding improvement program.

| S-EPMC7781923 | biostudies-literature

Next-generation sequencing of the complete mitochondrial genome of the Piao chicken (Gallus gallus).

Project description:In this study, the complete mitochondrial genome sequence of Piao chicken (Gallus gallus) was obtained by using the next-generation sequencing method for the first time. The complete mitogenome sequence of Piao chicken contains 2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNA genes and a D-loop region. This study serves as a valuable genetic resource for mitochondrial studies and can be used in understanding the maternal lineages of native chickens.

| S-EPMC7781869 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of Caridina multidentata and phylogenetic analysis.

Project description:In this study, the complete mitochondrial genome (mitogenome) of Caridina multidentata is reported for the first time. These data demonstrate that the C. multidentata mitochondrial genome is a 15,825 bp circular molecule and encodes the typical 37 metazoan mitochondrial genes [13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs)] and an A + T-rich control region. The genome composition was highly A + T biased 63.45% and showed negative AT-skew (-0.131) and slightly possitive GC-skew (0.018). The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for shrimps.

| S-EPMC7799520 | biostudies-literature

The complete mitochondrial genome and phylogenetic analysis of the Hetian chicken (Gallus gallus).

Project description:In this study, the complete mitochondrial genome of Hetian chicken (Gallus gallus) was obtained by using next generation sequencing method. The total length of complete mitogenome sequence is 16,784 bp, containing one control region, 2 ribosomal RNAs, 13 protein-coding genes and 22 transfer RNA genes. This work provides a valuable source of data for the study of the evolution of Gallus gallus mitochondrial genome and contributes to Hetian chicken breeding improvement program.

| S-EPMC7782330 | biostudies-literature

Complete mitochondrial genome and phylogenetic analysis of Huangshan Black chicken (Gallus gallus).

Project description:In this study, we sequenced the complete mitochondrial genome (mitogenome) of the Huangshan Black chicken (HBC). Results showed that the complete HBC mitogenome was 16,785 bp in size, comprising 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and 1 non-coding control region (D-loop). The overall nucleotide composition was 32.5% for C, 30.3% for A, 23.7% for T, and 13.5% for G. Phylogenetic analysis showed that the HBC mitogenome was clustered with Xianju chicken, which belonged to the haplogroup D2. Our results therefore demonstrate that the origin of HBC corresponds to haplogroup D2 distribution and might have at least one maternal lineage originated from Southeast Asia.

| S-EPMC7872527 | biostudies-literature

The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis.

Project description:The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.

| S-EPMC6679912 | biostudies-literature

Complete Mitochondrial Genome, Genetic Diversity and Phylogenetic Analysis of Pingpu Yellow Chicken (Gallus gallus).

Project description:In this study, the complete mitochondrial genome sequence of one female Pingpu Yellow chicken (PYC) and the D-loop sequences obtained from 60 chickens were analyzed to investigate their genetic diversity and phylogeny. The total length of the PYC mitogenome is 16,785 bp and that of the complete D-loop is 1231 to 1232 bp. The mitogenome comprises 22 transfer ribonucleic acids (tRNAs), 2 ribosomal ribonucleic acids (rRNAs), 13 protein-coding genes (PCGs), and 1 non-coding control region (D-loop). Additionally, the total length of the 13 PCGs is 11,394 bp, accounting for 67.88% of the complete mitogenome sequence, and the PCGs region has 3798 codons. A majority of the PCGs have ATG as the start codon. The haplotype and nucleotide diversity of PYC were 1.00000 ± 0.00029 and 0.32678 ± 0.29756, respectively. In the D-Loop data set, we found 25 polymorphic sites, which determined 18 haplotypes and 3 major haplogroups (A-C). Therefore, PYC has a classical vertebrate mitogenome, with comparatively high nucleotide diversity and potentially three maternal lineages. The neighbor-joining (NJ) tree analysis results showed PYC grouped with the Luhua (MT555049.1) and Nandan chickens (KP269069.1), which indicates that PYC is closely related to these two breeds.

| S-EPMC9654125 | biostudies-literature

Characterization and phylogenetic analysis of the complete mitochondrial genome in Xiaoxiang chicken (Gallus gallus domesticus).

Project description:Xiaoxiang chicken (Gallus gallus domesticus) is one of the native breeds in the Southeastern of Guizhou province, China. The complete mitochondrial genome sequence of Xiaoxiang chicken (small-sized breed chicken) was obtained for the first time. The mitogenome is 16,784 bp in length, and it contained a D-loop region, two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. A neighbour-joining phylogenetic tree was structured based on the D-loop, which indicated that the Red junglefowl was the direct ancestor of Xiaoxiang chicken, and both were closed to the Silky chicken and Dongan black chicken.

| S-EPMC7748485 | biostudies-literature

Characteristics of the complete mitochondrial genome of Douhua chicken (Gallus gallus) and phylogenetic considerations.

Project description:Douhua chicken is a unique local breed from Anhui Province, China. This study aimed to illustrate the Douhua chicken mitogenome and clarify its phylogenetic status by sequencing and annotating the complete mitochondrial genome using high-throughput sequencing and primer walking. Phylogenetic analysis through the Kimura 2-parameter model indicated the maternal origin of Douhua chicken. The results revealed that the mitochondrial genome is a closed circular molecule (16,785 bp) that consists of 13 protein-coding genes, 22 transfer RNA (tRNA) coding genes, two ribosomal RNA (rRNA) coding genes, and a control region. The base composition of the Douhua chicken mitogenome contains 30.3% A, 23.7% T, 32.5% C, and 13.5% G, and the haplotype and nucleotide diversity values are 0.829 (Hd) and 0.00441 (Pi), respectively. Furthermore, 10 haplotypes of D-loop sequences among 60 Douhua chickens were identified and distributed into four haplogroups (A, C, D, and E). Overall, the result of the present study indicates that Douhua chicken may have originated from Gallus gallus, and this process was influenced by Gallus gallus spadiceus, Gallus gallus murghi, and Gallus gallus bankiva. This study provides novel mitogenome data to support further phylogenetic and taxonomic studies on Douhua chicken. Additionally, the findings of this study will provide deeper insights for identifying the genetic relationships among populations and tracing maternal origins based on phylogenetic considerations for use in studies on the geographic conservation, utilization, and molecular genetics of poultry species.

| S-EPMC10016196 | 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