野骆驼基因组密码子偏好性分析

doi:10.16431/j.cnki.1671-7236.2023.02.001

摘要/Abstract

摘要： 【目的】密码子使用的偏好性普遍存在于几乎所有物种基因组中。试验旨在探究野骆驼(Camelus ferus)基因组密码子的使用偏好性和影响因素,为骆驼基因组研究和密码子优化提供依据。【方法】以野骆驼全基因组数据为材料,通过生物信息学、ENC-plot绘图、Neutrality-plot绘图和PR2-plot绘图等多种分析方法,对野骆驼蛋白质编码基因密码子的使用特性和影响因素进行分析,并与其他动物基因组的密码子偏好性进行比较研究。【结果】野骆驼基因组编码区的GC含量高于AT含量,密码子末位碱基较偏好以G/C结尾。相对同义密码子使用度(RSCU)＞1的有29个密码子,其中14个以C结尾,9个以G结尾。ENC-plot、Neutrality-plot和PR2-plot绘图分析结果表明,野骆驼基因组密码子的使用情况受自然选择和突变的双重影响,主要因素是自然选择。确定了15个主要以C或G结尾的最优密码子,分别为AUC、GGC、CUG、GUG、GCC、UCC、CCC、AGA、ACC、UAC、CAC、AGC、UUG、CAG和CGG。野骆驼与单峰驼、小鼠的密码子使用偏好性较为接近。【结论】野骆驼基因组密码子的使用情况受自然选择和突变的双重影响,导致密码子偏好性的主要因素为自然选择。研究结果可为野骆驼遗传种质资源保护和利用、基因工程、异源基因高效表达提供参考。

关键词: 野骆驼; 遗传密码; 密码子偏好性; 自然选择; 突变压力

Abstract: 【Objective】 Differential codon usage bias are prevalent in genomes of almost all species.In order to provide a basis for Camelus ferus genome research and codon optimization,the codon usage bias and influencing factors of Camelus ferus genome were analyzed.【Method】 The codon usage characteristics and influence factors of protein-coding genes of Camelus ferus genome were analyzed by various methods such as bioinformatics analysis,ENC-plot,Neutrality-plot and PR2-plot analysis.Meanwhile,the codon preferences between Camelus ferus and other species were analyzed.【Result】 The GC content was higher than AT content in the coding region of Camelus ferus genome,and the codon terminal bases were preferred to G/C.There were 29 codons with a relative synonymous codon usage (RSCU) greater than 1,of which 14 ended in C and 9 ended in G.The results of ENC-plot,Neutrality-plot and PR2-plot analysis showed that the codon usage bias were influenced by both natural selection and mutation,and the main factor was natural selection.Fiftheen optimal codons mainly ended with C or G were identified,including AUC,GGC,CUG,GUG,GCC,UCC,CCC,AGA,ACC,UAC,CAC,AGC,UUG,CAG and CGG.The codon usage bias of Camelus ferus, Camelus dromedarius and Mus musculus was relatively close.【Conclusion】 The codon usage bias in Camelus ferus genome was influenced by both natural selection and mutation,with natural selection played a greater influence.The results would provide reference and guidance for the protection and utilization of Camelus ferus genetic germplasm resources,genetic engineering and efficient expression of heterologous genes.

Key words: Camelus ferus; genetic codon; codon preference; natural selection; mutation pressure

中图分类号:

赵禹, 赵如莉, 郜原. 野骆驼基因组密码子偏好性分析[J]. 中国畜牧兽医, 2023, 50(2): 429-439.

ZHAO Yu, ZHAO Ruli, GAO Yuan. Analysis of Codon Preference in Camelus ferus Genome[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 429-439.

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