Mitochondrial PCGs Provide Novel Insights into Subspecies Classification, Codon Usage and Selection of Cervus canadensis Distributed in Qinghai and Gansu, China
文献类型： 外文期刊
作者： Dong, Shiwu 1 ; Tang, Lixin 1 ; Yang, Sukun 1 ; Chen, Xu 1 ; Feng, Yang 2 ; Wang, Xinhao 3 ; Su, Weilin 1 ; Xing, Xiumei 1 ;
作者机构： 1.Chinese Acad Agr Sci, State Key Lab Mol Biol Special Econ Anim, Inst Special Anim & Plant Sci, Changchun 130112, Peoples R China
2.Gansu Agr Univ, Coll Anim Sci & Technol, Lanzhou 730070, Peoples R China
3.Guangdong Chimelong Grp, Guangzhou 511400, Peoples R China
关键词： Cervus elaphus; Cervus canadensis kansuensis; phylogeny; mitochondrial characteristics; codon usage; natural selection
期刊名称：ANIMALS （ 影响因子：2.7； 五年影响因子：3.2 ）
ISSN： 2076-2615
年卷期： 2025 年 15 卷 10 期
页码：
收录情况： SCI
摘要： Although Cervus elaphus (Linnaeus, 1758) has been well studied, the subspecific taxonomy of Cervus canadensis populations in Qinghai and Gansu, China, is still controversial, and the mitochondrial characteristics of Cervus elaphus (Linnaeus, 1758) remain incompletely understood. We assembled 89 mitogenomes of C. canadensis from five geographical populations across Qinghai and Gansu. Phylogenetic analysis confirmed that the 89 individuals are taxonomically classified as C. c. kansuensis. Nucleotide compositions showed a higher abundance of adenine and cytosine compared to guanine and thymine in both complete mitogenomes and mitochondrial PCGs. Codon usage analysis revealed a strong preference towards A-ending codons (68.04% of over-represented codons, RSCU > 1.6) in mitochondrial PCGs, with systemic avoidance of G-ending codons (53.30% of unused codons, RSCU = 0). The CAMs of 13 PCGs are reported for the first time. Furthermore, the ENC plot showed that the codon usage of all PCGs was biased except for gene ATP8. The PR2 bias plot showed that gene ND6 exhibited bias towards T3 and G3, whereas the other genes preferred A3 and C3. Both the ENC-plot and PR2 bias plot suggested that natural selection played an important role in the forces driving codon usage bias in mitochondrial PCGs. Our results demonstrate the subspecific status of C. canadensis distributed in Qinghai and Gansu as C. c. kansuensis, and provide insights into the mitochondrial characteristics of C. c. kansuensis. The mitogenome sequences assembled in this study provide valuable data for further understanding of the Cervus elaphus (Linnaeus, 1758) mitogenome.
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