The complete mitochondrial genome of the Gongxi chicken and its phylogenetic analyses

Abstract

Gongxi chicken (GXC) is one of the famous indigenous breed of Hunan province in China. It is the first time that the complete mitochondrial genome sequence of the GX was reported. The total length of the mtDNA is 16,783 bp. It contains the typical structure, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and 1 noncoding control region (D-loop region). The overall composition of the mtDNA was estimated to be 30.30% for A, 23.75% for T, 32.48% for C and 13.47% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed 26 Galliformes species are divided into four major clades: Phasianidae, Numidiidae, Odontophoridae and Megapodiidae. In addition, our work confirmed that GXC and Dongan yellow chicken (DYC), Taoyuan chicken and Dongan black chicken have a close genetic relationship with fellow tribal members Xuefeng black-boned chicken and Huang Lang chicken. Meanwhile, we also found that GXC and DYC have highly similar genetic relationship. This work will provide an important data set for the study in genetic mechanism of chicken in Hunan province.

Keywords:

• Gongxi chicken
• mitochondrial
• phylogenetic analyses

Domestic chicken (Gallus gallus domesticus) play a key role in the agricultural and economic sectors in Hunan Province of China. There are numerous domestic chicken breeds in Hunan Province, including: Gongxi chicken (GXC), Dongan yellow chicken (DYC), Taoyuan chicken (TYC), Huang Lang chicken (HLC), Xuefeng black-boned chicken (XBC) and Dongan black chicken (DBC) (Liu et al. 2016a,b; Yu et al. 2016; Peng et al. 2018). However, a better characterization of the genetic diversity of these domestic chicken breeds is in urgent need to increase the conservational application for them in Hunan province. In addition, only the complete mitochondrial genome of GXC has not been reported. The features of GXC is good growth performance and meat quality. In this study, we newly determined the complete mitochondrial genome of GXC, and the adult individuals of GXC were collected at its originally breeding farm in Xinhuang Dong Autonomous County (27.11 N and 109.17 E), Hunan Province, China on June 2018. And the specimens were stored at −80 °C in our laboratory (Research Department of Animal Nutrition and Poultry, Hunan Institute of Animal and Veterinary Science). Total genomic DNA was extracted from the thigh muscle of a single individual using the EasyPure Kit of Genomic DNA (Transgen Biotech, Beijing, China). Whole mitochondrial genome was amplified with 13 pairs of primers and sequenced by BioSune Biotech (Shanghai, China). DNA sequence was analyzed using DNAStar.Lasergene.v7.1 software (Madison, WI), tRNA Scan-SE1.21 software (Lowe and Eddy 1997) and DOGMA software (Wyman et al. 2004).

The total length of the mtDNA is 16,783 bp. It contains the typical structure, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region) (GenBank accession No. MH879470). The overall composition of the mtDNA was estimated to be 30.30% for A, 23.75% for T, 32.48% for C and 13.47% for G. Besides the COX1 initiation codon is GTG, and the rest of the proteins are ATG. All these genes have 15 spaces and 6 overlaps both in the length of 1–10 bp. These genes had four types of termination codons, including TAA, AGG, AGA and an incomplete termination codon ‘‘T– –’’. ‘‘T– –’’ is the 5' terminal of the adjacent gene (Anderson et al. 1981). Among 13 protein-coding genes, the longest one was ND5 gene (1818 bp), which was located between the tRNA^Leu and Cytb, and the shortest one was ATPase8 gene (165 bp), which was located between the tRNA^Lys and ATPase6.

Phylogenetic analysis was performed using the complete mitochondrial DNA sequences of 26 Galliformes. Each of the sequence dataset was aligned by ClustalX (Thompson et al. 1997) and analyzed by neighbor-joining (N-J) in MEGA 4.0 (Tamura et al. 2007), and bootstrap analysis was performed with 100 replications. An N-J tree showed that the analyzed species are divided into four major clades (Figure 1). Phasianidae makes up the first lineage, which is sister to the second group, Numidiidae; Odontophoridae forms the third group and is sister to Megapodiidae and Numidiidae. The lineage consisting of these three groups in turn is sister to the fourth clade, Megapodiidae. In addition, our work confirmed that GXC and DYC, TYC and DBC have a close genetic relationship with fellow tribal members XBC and HLC which are consistent with those as reported previously (Zhao et al. 2016). Meanwhile, we also found that GXC and DYC have highly similar genetic relationship.

Figure 1. Phylogenetic analysis based on complete mitochondrial genome sequences. An N-J tree was built based on the phylogenetic analysis of 26 Galliformes species’ complete mitochondrial genomes. The mitochondrial genome sequences of the Galliformes species were obtained from the GenBank databases (Accession numbers have marked on the figure). Abbreviation of species indicates: DBC, Dongan black chicken; TYC, Taoyuan chicken; GXC: Gongxi chicken; DYC: Dongan yellow chicken; XBC, Xuefeng black-boned chicken; HLC, Huang Lang chicken.

Disclosure statement

The authors report no conflicts of interest.

Additional information

Funding

This research was supported by International S&T Cooperation Program of China (ISTCP, 2013DFG31810) and Science & Technology Project of Hunan Province (HHN2017SC09).