中国古老月季“月月粉”的叶绿体基因组密码子偏好性分析  

Analysis on Chloroplast Genome Codon Usage Bias of Rosa chinensis Cultivar Old Blush

作　　者：侯哲 李昂 黄长兵[1] HOU Zhe;LI Ang;HUANG Changbing(Suzhou Polytechnic Institute of Agriculture,Suzhou Jiangsu 215008,China)

机构地区：[1]苏州农业职业技术学院,江苏苏州215008

出　　处：《种子》2023年第1期58-64,109,共8页Seed

基　　金：江苏省种业振兴“揭榜挂帅”项目(JBGS[2021]091);苏州农业职业技术学院博士提升计划科研启动基金项目资助(BS[2022]08);江苏省林业科技创新与推广项目(LYKJ[2021]02);中央财政林业改革发展资金项目(苏[2022]TG10);苏州市科技计划(农业科技创新)面上项目(SNG2022025);四川省自然科学基金(2022NSFSC1141)。

摘　　要：本研究基于“月月粉”月季叶绿体全基因组图谱,对其密码子偏好性进行分析。结果表明,月季的叶绿体基因组总长为156591 bp,具有典型的四分体结构。共筛选到49条基因序列用于密码子偏好性分析,GC 1,GC_(2),GC_(3)的平均值分别为47.74,39.38,29.16,密码子第一位的GC含量最大,第三位的最小,具有明显的差异;有效密码子数(ENC)与第三位密码子的GC含量显著相关;中性绘图结果说明GC^(3)与GC_(12)的相关性不显著,且密码子的偏好性受自然选择的影响;ENC-plot及ENC比值频数分布结果表明,大多数基因的ENC值低于预期值,大多数基因位于-0.05~0.05区间外,说明大部分基因受到了突变的影响;同义密码子相对使用度(RSCU)分析表明,RSCU值大于1的密码子大多数以A/U结尾,同时选取RSCU值大于1且ΔRSCU值大于等于0.08的密码子作为最优密码子,即UUU、CUU、AUA、CAU、GAU、UCA、ACA、CGA、AGU、AGA、CGA,共计11个最优密码子,且这11个最优密码子均以A和U结尾。In this study,the codon bias of Rosa chinensis based on the whole genome map of its chloroplasts was analysed.The results showed that the total length of the chloroplast genome of R.chinensis was 156591 bp,forming a typical tetrad structure.A total of 49 gene sequences were screened for codon bias analysis,and the mean values of GC 1,GC_(2)and GC_(3)were 47.74,39.38 and 29.16 respectively,with the largest GC content in the first codon and the smallest in the third,with significant differences;the effective codon number(ENC)was significantly correlated with the GC content in the third codon;the neutral mapping results indicated that the correlation between GC_(3)and GC_(12)was not significant,and the codon bias was affected by natural selection;the ENC-plot and ENC ratio frequency distribution results showed that the ENC values of most genes were lower than expected,and most genes were located outside the-0.05-0.05 interval,indicating that most genes were affected by mutations;the relative synonymous codon usage analysis showed that most of the codons with RSCU values>1 ended in A/U,while codons with RSCU values>1 andΔRSCU values≥0.08 were selected as the optimal codons,which were UUU,CUU,AUA,CAU,GAU,UCA,ACA,CGA,AGU,AGA,and CGA,a total of 11 optimal codons,and all these 11 optimal codons ended with A and U.

关 键 词：月季 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：S685.12[农业科学—观赏园艺]