石潭鸡与中国地方鸡种mtDNA密码子偏好性分析

doi:10.16431/j.cnki.1671-7236.2025.12.022

摘要/Abstract

摘要： 【目的】分析石潭鸡与中国其他地方鸡种线粒体DNA(mtDNA)基因序列的密码子使用模式及特性，探究石潭鸡与中国主要地方鸡种的进化关系。【方法】获取10只健康成年石潭鸡的mtDNA基因序列，采用CodonW 1.4.2软件分析其与中国17个地方鸡种mtDNA基因密码子使用偏好性，计算密码子偏好参数，并进行偏好性密码子的聚类分析、氨基酸分析、因子相关性及基因序列的聚类分析。【结果】石潭鸡与中国主要地方鸡种的mtDNA序列均倾向于使用以C碱基结尾的密码子，而以G碱基结尾的密码子使用频率较低。石潭鸡以CGA、CUA、ACC、UUC等27个密码子的相对密码子使用度(RSCU)均＞1，为偏好性密码子。石潭鸡与桃源鸡、五华三黄鸡、广西三黄鸡、如皋黄鸡、海南文昌鸡、河田鸡和皖南三黄鸡的密码子偏好性相近，进一步选取上述7个鸡种展开分析，明确石潭鸡与该群体在遗传层面的关联特征，氨基酸组成分析显示，石潭鸡线粒体中亮氨酸含量最高，其次为异亮氨酸和苏氨酸，8个鸡种以AC和GU结尾的密码子呈现明显分化，且AC结尾密码子的含量较高。基于mtDNA基因序列的聚类分析发现，石潭鸡与如皋黄鸡的亲缘关系最近。【结论】石潭鸡与中国主要地方鸡种mtDNA序列均表现出以C碱基结尾密码子的显著偏好，且AC结尾的密码子含量相对较高；石潭鸡线粒体中亮氨酸含量最高，与如皋黄鸡的亲缘关系最近。

关键词: 石潭鸡; mtDNA; 密码子偏好性; 进化分析

Abstract: 【Objective】 This study aimed to analyze the codon usage patterns and characteristics of mitochondrial DNA (mtDNA) gene sequences in Shitan chickens and native chicken breeds of China,and explore the evolutionary relationship between Shitan chickens and main native chicken breeds of China. 【Method】 mtDNA gene sequences from 10 healthy adult Shitan chickens were obtained.CodonW 1.4.2 software was used to analyze the codon usage bias of mtDNA gene in Shitan chickens and 17 native chicken breeds of China,and codon preference parameters were calculated.Subsequently,cluster analysis of preferred codons,amino acid analysis,factor correlation analysis,and cluster analysis of gene sequences were performed. 【Result】 Both Shitan chickens and main native chicken breeds of China exhibited a preference for codons ending with C in mtDNA sequences,while codons ending with G were used less frequently.In Shitan chickens,27 codons including CGA,CUA,ACC,and UUC had a relative synonymous codon usage (RSCU) value greater than 1,indicating they were preferred codons.Shitan chickens showed similar codon usage bias with Taoyuan chickens,Wuhua Sanhuang chickens,Guangxi Sanhuang chickens,Rugao Yellow chickens,Hainan Wenchang chickens,Hetian chickens,and Wannan Sanhuang chickens.Consequently,these seven breeds,along with Shitan chickens,were selected for further analysis to clarify the genetic relationship.Amino acid composition analysis revealed that leucine was the most abundant amino acid in mitochondria of Shitan chickens,followed by isoleucine and threonine.Among these eight chicken breeds, AC- and GU- ending codons showed significant divergence,with AC-ending codons being significantly more prevalent.Cluster analysis based on mtDNA gene sequences indicated that Shitan chickens was phylogenetically closest to Rugao Yellow chickens. 【Conclusion】 Shitan chickens and maind native chicken breeds of China exhibited a significant preference for C-ending codons,with notably higher usage of AC-ending codons.Leucine was the most abundant amino acid in mitochondria of Shitan chickens.Shitan chickens shared the closest genetic relationship with Rugao Yellow chickens.

Key words: Shitan chickens; mtDNA; codon usage bias; evolutionary analysis

中图分类号:

S813.3

张梦萍, 林明昕, 吴忠亮, 罗景飞, 陈珊对儿, 吴琼. 石潭鸡与中国地方鸡种mtDNA密码子偏好性分析[J]. 中国畜牧兽医, 2025, 52(12): 5772-5784.

ZHANG Mengping, LIN Mingxin, WU Zhongliang, LUO Jingfei, CHEN Shanduier, WU Qiong. Analysis of mtDNA Codon Usage Bias in Shitan Chickens and Native Chicken Breeds of China[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(12): 5772-5784.

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