The complete mitochondrial genome of the Zhijiang duck and its phylogenetic analyses

Abstract

Zhijiang duck (ZJ) is one of the famous indigenous breed of Hunan province in China. The complete mitochondrial genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. It is the first time that the complete mitochondrial genome sequence of the ZJ was reported. The total length of the mtDNA is 16,604 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). The overall composition of the mtDNA was estimated to be 29.22% for A, 22.20% for T, 32.82% for C, and 15.77% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed 20 Anseriform species are divided into four major clades: Anatinae, Anserinae, Dendrocygninae, and Anseranatidae. In addition, our work confirmed that ZJ and Anas poecilorhyncha have a close genetic relationship with fellow tribal members Linwu duck and Youxian duck. Meanwhile, we also found that ZJ and A. poecilorhyncha have highly similar genetic relationship. This work will provides an important data set for the study in the genetic mechanism of duck in Hunan province.

Keywords:

• Zhijiang duck
• mitochondrial
• phylogenetic analyses

Domestic duck plays a key role in the agricultural and economic sectors in Hunan Province of China. There are numerous domestic duck breeds in Hunan Province, including Linwu duck (LW), Youxian duck (YX), and Zhijiang duck (ZJ) (Lin, Jiang, et al. 2016; Lin, Qiu, et al. 2016). However, a better characterization of the genetic diversity of these domestic duck breeds is in urgent need to increase their conservational application in Hunan province. In addition, only the complete mitochondrial genome of ZJ has not been reported. The features of ZJ is less subcutaneous fat deposition and good meat quality. In this study, we newly determined the complete mitochondrial genome of ZJ, and the adult individuals of ZJ were collected at its originally breeding farm in Zhijiang Dong Autonomous County (27.15 N and 109.30 E), Hunan Province, China, on May 2018. 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 thorax 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 16,604 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. MH744426). The overall composition of the mtDNA was estimated to be 29.22% for A, 22.20% for T, 32.82% for C, and 15.77% for G. Besides the COX1, COX2, ND5 initiation codon is GTG, ND6 is CTA, and the rest of the proteins are ATG. All these genes had 14 spaces and 8 overlaps both in the length of 1–10 bp. These genes had four types of termination codons, including TAG, TAA, AGG, 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 (1824 bp), which was located between the tRNA^Leu and Cytb, and the shortest one was ATPase8 gene (168 bp), which was located between the tRNA^Lys and ATPase6.

Phylogenetic analysis was performed using the complete mitochondrial DNA sequences of 20 Anseriform. 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). Anatinae makes up the first lineage, which is sister to the second group, Anserinae; Dendrocygninae forms the third group and is sister to Anatinae and Anserinae. The lineage consisting of these three groups in turn is sister to the fourth clade, Anseranatidae. In addition, our work confirmed that ZJ and Anas poecilorhyncha have a close genetic relationship with fellow tribal members Linwu duck and Youxian duck which are consistent with those as reported previously (He et al. 2015). Meanwhile, we also found that ZJ and A. poecilorhyncha 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 20 Anseriform species’ complete mitochondrial genomes. The mitochondrial genome sequences of the Anseriform species were obtained from the GenBank databases (Accession numbers are marked in the figure). Abbreviation of species indicates: LW: Linwu duck; YX: Youxian duck; ZJ: Zhijiang duck.

Disclosure statement

No potential conflict of interest was reported by the author.

Additional information

Funding

This research was supported by National Waterfowl Industry Technology System [CARS-42].