3种木薯全基因组的密码子偏好性模式与变异来源比较  

Comparison of codon preference patterns and variation sources in Manihot esculenta Crantz genomes

作　　者：王占军 丁亮 蔡倩文 李杰 吴子琦 姚怀桐 王悦 焦春燕 欧祖兰 徐忠东 施季森[2] 陈金慧[2] WANG Zhanjun;DING Liang;CAI Qianwen;LI Jie;WU Ziqi;YAO Huaitong;WANG Yue;JIAO Chunyan;OU Zulan;XU Zhongdong;SHI Jisen;CHEN Jinhui(School of Life Sciences,Hefei Normal University,Hefei 230601,China;Key Laboratory of Forest Genetics&Biotechnology of Ministry of Education,Co-Innovation Center for Sustainable Forestry in Southern China,Nanjing Forestry University,Nanjing 210037,China)

机构地区：[1]合肥师范学院生命科学学院,合肥230601 [2]南京林业大学林木遗传和生物技术省部共建教育部重点实验室/南京林业大学南方现代林业协同创新中心,南京210037

出　　处：《应用与环境生物学报》2021年第4期1013-1021,共9页Chinese Journal of Applied and Environmental Biology

基　　金：国家自然科学基金项目(32071784);安徽省自然科学基金项目(1708085MC76);安徽省高校优秀青年人才支持计划项目(gxyq2020040);安徽省高等学校省级质量工程项目(2020szsfkc0744,2020jyxm1566);江苏省高校优势学科建设工程项目(PAPD)资助。

摘　　要：密码子偏好性研究有利于了解基因表达特征、探索遗传进化规律及为分子育种提供依据.综合运用Perl语言和Codon W1.4.2、SPSS23.0等软件,系统分析3种木薯基因组的编码基因序列,从而得出密码子使用特征并明确影响密码子使用的变异来源.结果显示,3种木薯基因组的密码子在使用模式上具有较高的相似性:总碱基组成在3种木薯中差异较小,都是A/T含量较高,而G/C含量较低,且均偏好使用A/T结尾;通过RSCU(同义密码子相对使用度)值比较分析发现,3种木薯有27个共同的偏好密码子,其中以A/T结尾的密码子达85%以上;RFSC(同义密码子相对使用频率)值显示出3种木薯具有14个相同的高频密码子;其基因的异源表达受体优先选择拟南芥、烟草和毛果杨;密码子偏好性主要受自然选择影响,同时也受到突变压力等其他因素的影响.本研究表明3种木薯基因组的密码子使用模式高度相似且主要受自然选择影响,结果可为将来研究木薯的进化规律和提高外源基因表达效率提供重要依据.The study of codon usage bias is helpful in understanding the gene expression characteristics and exploring the genetic evolution rule,which provides the basis for molecular breeding.In this study,Perl,Codon W 1.4.2,and SPSS 23.0,were used to systematically analyze the coding DNA sequences of the three cassava genomes,so the characteristics of codon usage and the sources of variation affecting the usage were identified.The results showed that the codon usage patterns of the three cassava genomes were highly similar.The total base composition of the three cassava genomes showed little difference,all with a higher A/T content and a lower G/C content,with a tendency to use the A/T ending codons.We have found that there were 27 common codons in the three cassava species,and more than 85%codons ending with A/T based on the relative synonymous codon usage(RSCU)values.The relative frequency synonymous codon(RFSC)values showed that there were 14 identical highfrequency codons in the three cassava species;the heterologous expression receptors of cassava genes is present in Arabidopsis thaliana,tobacco,and poplar.The codon usage pattern is mainly affected by natural selection,but also by other factors such as mutation pressure.In this study,the codon usage patterns of the three cassava genomes are highly similar and mainly affected by natural selection,which provides an important basis for the further studies on the evolutionary rules and improves the expression efficiency of heterologous genes in cassava.

关 键 词：木薯 全基因组序列 密码子偏好性 进化规律 异源表达 

分 类 号：S533[农业科学—作物学]