木薯叶绿体基因组密码子偏好性分析  

Analysis of Codon Usage Bias in Chloroplast Genome of Cassava

作　　者：赵英[1] 付海天[1] 金刚[1] 徐钏 宋恩亮[1] 罗燕春[1] 莫永龙[1] ZHAO Ying;FU Hai-tian;JIN Gang;XU Chuan;SONG En-liang;LUO Yan-chun;MO Yong-long(Guangxi Subtropical Crop Research Institute,Nanning 530001,China)

机构地区：[1]广西壮族自治区亚热带作物研究所,广西南宁530001

出　　处：《江西农业学报》2022年第4期46-52,共7页Acta Agriculturae Jiangxi

基　　金：国家重点研发计划(2019YFD1001100);广西农业科学院基本科研业务专项(桂农科2021YT149);广西重点研发计划项目(桂科AB16380163);广西重点研发计划(桂科AB21196071)。

摘　　要：利用Codon W等软件,对木薯叶绿体基因组55条蛋白编码序列的密码子进行了分析。发现木薯叶绿体基因组密码子的GC分布不均匀,平均含量为37.81%,其中GC1、GC2、GC3的含量分别为46.64%、39.19%和27.58%;GC3s的平均含量为24.46%,表明木薯叶绿体密码子中A或T的使用频率高于G和C。有效密码子数(ENC)的平均值为47.57,说明木薯叶绿体基因组密码子的偏好性较弱。中性绘图、ENC-plot和PR2-plot分析结果表明木薯叶绿体基因组密码子的使用偏好主要受选择的影响。RSCU>1的密码子共有30个,其中97%的密码子以A或T结尾,再次证明木薯偏爱使用以A或T结尾的密码子。筛选出最优密码子9个,分别是TTG、TCA、CCA、CAT、AAT、GAT、CGA、AGA、GGA。Codon usages of 55 chloroplast genes in cassava were analyzed by the Codon W and related software.The results showed that average GC content of the cassava chloroplast genes was 37.81%,and the average GC content of three positions of the gene codons was 46.64%,39.19%and 27.58%.GC3s content of gene condons was 24.46%,indicating that synonymous codons in chloroplast genome tend to end with A/T.The average ENC was 47.57,indicating that the condon bias was weak.Neutral mapping analysis,PR2-plot and ENC-plot analysis demonstrated that the codon preference of cassava chloroplast genome was mainly affected by selection.There were 30 codons with RSCU>1,97%of which ended in A or T,again indicating that synonymous codons in chloroplast genome tend to end with A/T.Nine optimal codons were finally determined,which were TTG,TCA,CCA,CAT,AAT,GAT,CGA,AGA and GGA.

关 键 词：木薯 叶绿体基因组 密码子 使用偏好性 最优密码子 

分 类 号：S533[农业科学—作物学]