牦牛与普通牛、水牛的X染色体基因编码区比较及密码子偏性分析

Comparison of X Chromosome Gene Coding Regions and Analysis of Codon Bias in Bos grunniens,Bos taurus and Bubalus bubalis

【目的】从基因组比对及密码子偏性角度分析牦牛与其他牛亚科动物X染色体,有助于了解牦牛品种差异及系统进化地位,为其适应高原低压低氧环境和密码子优化提供参考。【方法】以牦牛X染色体参考基因编码区序列为参考,与普通牛和江河型水牛X染色体参考基因编码区序列进行基因组比对和基因共线性分析,同时进行基因注释,对过滤后的编码区文件进行相对同义密码子使用频率(RSCU)、ENC-plot、PR2-plot和最优密码子确定等偏性分析。【结果】在牦牛X染色体基因编码区发现了参与气管收缩、肺部呼吸及机体代谢等基因与普通牛和水牛存在差异,如KLHL13、CENPI和PGK1等基因;共线性显示长段由强选择压和突变压下表现出的交换线性区域;密码子分析中3种牛亚科动物密码子使用偏性相似,偏性均较弱,均偏向G/C结尾;强偏性密码子(RSCU≥1.5)均为CUG、GUG、AGA、AGG和UGA;牦牛、普通牛和水牛分别筛选出16、13和9个最优密码子,均以A/U结尾。【结论】牦牛与普通牛、水牛相比面临了更大的选择压力,累计的变异程度更大,三者的密码子偏性受到自然选择作用均大于突变作用。研究结果为牦牛的遗传育种、密码子优化和遗传资源开发利用提供参考。

【Objective】Analyzing the X chromosome of Bos grunniens and other subfamilies of cattle from the perspective of genome alignment and codon bias was helpful to understand the variety differences and phylogenetic status of Bos grunniens,and provided reference for its adaptation to high altitude low-pressure and hypoxia environment and codon optimization.【Method】Taking the coding region sequence of Bos grunniens X chromosome reference gene as the reference panel,genome alignment and gene collinearity analysis were carried out with the coding region sequence of X chromosome reference gene of Bos taurus and Bubalus bubalis.At the same time,gene annotation was carried out.The filtered coding region files were analyzed for preference,such as relative synonymous codon usage(RSCU),ENC-plot,PR2-plot and optimal codon determination.【Result】In the coding region of X chromosome gene of Bos grunniens,genes involved in tracheal contraction,lung respiration and body metabolism were found to be different from Bos taurus and Bubalus bubalis,such as KLHL13,CENPI and PGK1 genes.The collinearity results indicated that the long segment showed an exchange linear region due to strong natural selection and mutation pressure.In codon analysis,the codon usage bias of three species of bovine subfamily was similar,their bias was weak,and their codons were biased towards the end of G/C.Their strong biased codons(RSCU≥1.5)were all CUG,GUG,AGA,AGG and UGA.Among them,16 optimal codons were selected for Bos grunniens,13 for Bos taurus and 9 for Bubalus bubalis.These codons all end in A/U.【Conclusion】By comparing Bos taurus and Bubalus bubalis,Bos grunniens might be under greater natural selection,so its cumulative degree of variation in the process of evolution was also greater.The codon bias of Bos grunniens,Bos taurus and Bubalus bubalis were more affected by natural selection than mutation.These results would provide reference and guidance for Bos grunniens genetic breeding,codon optimization and the development and utilization of genetic resources.