Jin Sihua, Xia Jingjing, Jia Fumin, Jiang Lijun, Wang Xin, Liu Xuling, Liu Xing, Geng Zhaoyu
College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China.
Animals (Basel). 2022 Nov 4;12(21):3037. doi: 10.3390/ani12213037.
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.
在本研究中，分析了一只雌性平埔黄鸡（PYC）的完整线粒体基因组序列以及从60只鸡中获得的D-loop序列，以研究它们的遗传多样性和系统发育。PYC线粒体基因组的总长度为16,785 bp，完整D-loop的长度为1231至1232 bp。线粒体基因组包括22个转移核糖核酸（tRNA）、2个核糖体核糖核酸（rRNA）、13个蛋白质编码基因（PCG）和1个非编码控制区（D-loop）。此外，13个PCG的总长度为11,394 bp，占完整线粒体基因组序列的67.88%，PCG区域有3798个密码子。大多数PCG以ATG作为起始密码子。PYC的单倍型和核苷酸多样性分别为1.00000±0.00029和0.32678±0.29756。在D-Loop数据集中，我们发现了25个多态性位点，确定了18个单倍型和3个主要单倍群（A-C）。因此，PYC具有典型的脊椎动物线粒体基因组，具有较高的核苷酸多样性和潜在的三个母系谱系。邻接法（NJ）树分析结果显示，PYC与芦花鸡（MT555049.1）和南丹鸡（KP269069.1）聚类，这表明PYC与这两个品种密切相关。
