Abstract:

Codon preference is present in the genomes of almost all known species. In order to understand the codon use preference of Vitis vinifera genome and improve the efficiency of gene heterologous expression， the characteristics and influencing factors of coding gene codons in Vitis vinifera were studied and analyzed using genome-wide data of Vitis vinifera as the basic material， and the codon preference were compared with other expression systems and plant genomes of Vitis vinifera subfamily. The results showed that， based the chromosome sequence of grape， 21 887 coding sequences were screened out for analyzing the codons preference. The GC content of the codon in encoding gene of Vitis vinifera showed GC₁ （50.19%）>GC₃ （43.92%）>GC₂ （40.36%）， and the last base of codon was preferred to A/U. The 19 optimal codons were identified， including GCA， GCU， GAU， UUU， GGA， GGU， CAU， AUU， CUU， AAU， CCA， CCU， CAA， UCA， UCU， ACA， ACU， GUU， UAU， among which 6 codons ended with A and 13 codons ended with U. The preference of Vitis vinifera genomic codon was influenced by natural selection and mutation， and the natural selection was the main factor. Above results provided a theoretical basis for the study of grape genomics， and also provided guidance for improving the expression of heterologous proteins in Vitis vinifera and the in vitro expression of Vitis vinifera-related proteins.

Key words: Vitis vinifera, genetic code, codon preference, natural selection, mutation pressure

摘要：

密码子偏好性存在于几乎所有已知物种基因组中。为了解葡萄基因组的密码子使用偏好性并提高基因异源表达效率，以葡萄的全基因组数据作为基础材料，对葡萄编码基因密码子的特性和影响因素进行分析，并与其他表达系统和葡萄亚科植物基因组的密码子偏好性进行比较。结果表明，以葡萄染色体序列为研究对象，共筛选出21 887条编码序列的密码子。葡萄基因密码子不同位置的GC含量表现为GC₁（50.19%）>GC₃（43.92%）>GC₂（40.36%），密码子末位碱基较偏好于A/U。确定了19个最优密码子，分别为GCA、GCU、GAU、UUU、GGA、GGU、CAU、AUU、CUU、AAU、CCA、CCU、CAA、UCA、UCU、ACA、ACU、GUU、UAU，其中以A结尾的有6个，以U结尾的有13个。葡萄基因组密码子的使用受自然选择和突变的双重影响，其中导致葡萄基因组密码子偏好性的主要因素为自然选择。以上结果为葡萄基因组学的研究提供了理论基础，也为提高异源蛋白在葡萄中的表达和葡萄相关蛋白的体外表达提供了指导。

关键词: 葡萄, 遗传密码, 密码子偏好性, 自然选择, 突变压力