亚洲带绦虫基因组密码子使用偏性分析  

Analysis of Codon Usage Bias in Taenia asiatica Genome

作　　者：杨兴 刘西 盛梦诗 刘秋艳 姜丹丹 YANG Xing;LIU Xi;SHENG Meng-shi;LIU Qiu-yan;JIANG Dan-dan(College of Basic Medicine,Dali University,Dali,Yunnan,671000,China)

机构地区：[1]大理大学基础医学院,云南大理671000

出　　处：《动物医学进展》2021年第7期57-63,共7页Progress In Veterinary Medicine

基　　金：云南省科技厅应用基础研究项目(2017FD139);大理大学博士科研启动费项目(KYBS201604);大理大学大学生创新创业训练计划项目(XSXL2019006)。

摘　　要：为了解亚洲带绦虫基因组的密码子用法及影响密码子使用模式的主要因素,以亚洲带绦虫基因组注释的13323条CDS序列为数据来源,利用CodonW软件对其密码子碱基组成、有效密码子数(ENC)和同义密码子相对使用频率(RSCU)各项指标进行统计分析。结果显示:①从亚洲带绦虫基因组数据中筛选获得11203条CDS序列,平均长度为1386 bp,GC含量在25.9%~74.1%之间,变化范围较大;②同义密码子第3位出现G或C的频率为50.11%,比出现A或T的频率高;③有效密码子数介于20.64~61.00,平均为51.06;④ENC-plot分析、中性分析、PR2分析及相关性分析结果表明,影响亚洲带绦虫密码子使用偏性的因素除了突变和选择两种力量外,还包括GC含量、基因长度、蛋白质的亲水性和芳香度;⑤最终共有25个密码子被确定为最优密码子,绝大部分以G或C结尾。结果说明,亚洲带绦虫基因组中大部分基因密码子使用偏性较弱,仅少部分基因具有较强偏性,偏好使用以G或C结尾的密码子,且这一现象是由突变、选择、碱基组成等多重因素共同作用形成的,该结果为进一步研究该物种遗传背景和分子进化提供了一定的科学依据。In order to understand the codon usage pattern of Taenia asiatica genome and probe into the main factors affecting codon usage bias,a total of 13323 coding DNA sequences in Taenia asiatica genome were used as data source.Codon composition,effective number of codons(ENC)and relative synonymous codon usage(RSCU)were analyzed using CodonW software.The results showed as:①11203 CDS sequences were selected from Taenia asiatica genome database,there average length was 1386 bp.GC content of these genes ranged from 25.9%-74.1%and varied greatly in intensity.②Occurrence frequency of G or C in the third position of synonymous codon was 50.11%,which was higher than that of A or T.③The effective number of codon of Taenia asiatica genome ranged from 20.64-61.00,with the average of 51.06.④According to ENC plot,neutrality plot,PR2-Bias plot and correspondence analysis,we know that mutational and selective forces are probably driving factors of codon usage bias in Taenia asiatica genome.Meanwhile,other factors such as GC cotent,protein length,the GRAVY and aromaticity of each protein also influence codon usage.⑤Finally,a total of 25 codons were determined to be optimal codons,22 of which ending in G or C.The results indicated that the codon usage bias for most of genes is weak in Taenia asiatica,but a few of genes show stronger codon usage bias,and prefer codons ending with G or C.Meanwhile,the codon usage bias is formed under effect of mutation,selection,base composition etc.The above results would provide a good basis for the further study of the genetic background and molecular evolution of Taenia asiatica.

关 键 词：亚洲带绦虫 基因组 密码子使用偏性 最优密码子 

分 类 号：S852.734[农业科学—基础兽医学]