Characterization and phylogenetic evolution of mitochondrial genome in Tibetan chicken
Characterization and phylogenetic evolution of mitochondrial genome in Tibetan chicken
复制标题
藏鸡线粒体基因组的特征和系统发育进化。
DOI：
10.1080/10495398.2020.1858846
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发表时间：
2020-12-03
影响因子：
3.7
通讯作者：
Gao, Yushi
中科院分区：
文献类型：
--
作者：
Jia, Xiaoxu;Lu, Junxian;Gao, Yushi
本研究的目的是研究藏鸡线粒体基因组的特征和系统进化。本研究利用D-loop测序技术，对藏鸡（n= 40）进行了4种单倍型的鉴定，并选取4种单倍型的代表性个体进行线粒体全基因组测序，结合已发表的红原鸡线粒体基因组数据进行分析。四个单倍型属于三个以前发表的分支，即，进化枝A、进化枝B和进化枝E。基于D-loop测序数据，平均单倍型多样性和核苷酸多样性分别为0.658 ± 0.065和0.00442 ± 0.00094。藏鸡线粒体基因组全长16，785 bp，由22个转运RNA（transfer RNA，tRNA）基因、2个核糖体RNA（ribosomal RNA，rRNA）基因、13个蛋白质编码基因和1个非编码控制区（non-coding control region，CR）组成。与线粒体基因组相比，基于D-loop序列构建的系统发育树分布杂乱，未观察到藏鸡的品种聚类模式。结果表明，本研究中的藏鸡群体具有相对较低的核苷酸和单倍型多样性，可能共享多个母系谱系。与完整的线粒体基因组相比，D-环序列在解决系统发育关系方面的能力有限。
The objective of this study was to characterize mitochondrial genome and investigate phylogenetic evolution in Tibetan chicken. In this study, four haplotypes were identified based on D-loop sequencing in Tibetan chicken (n= 40), and each representative of four haplotypes was selected for total mitochondrial genome sequencing and analyzed together with published mitochondrial genome data of red jungle fowl. Four haplotypes belonged to three previously published clades, i.e., Clade A, clade B and clade E. Based on D-loop sequencing data, the average haplotype diversity and nucleotide diversity were 0.658 ± 0.065 and 0.00442 ± 0.00094, respectively. The mitochondrial genome of Tibetan chicken is 16,785 bp in size, consisting of 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein-coding genes and one non-coding control region (CR). Compared with the mitochondrial genome, a phylogenetic tree based on the D-loop sequence had a messy distribution, and no breed cluster pattern was observed in Tibetan chicken. The results indicate that Tibetan chicken populations in our study have relatively low nucleotide and haplotype diversity and likely share multiple maternal lineages. The D-loop sequence has limited power for the resolution of phylogenetic relationships in comparison with the complete mitochondrial genome.