圆锥南芥叶绿体基因组特征及密码子偏好性分析  

Analysis of Chloroplast Genome Characteristics and Codon Usage Bias of Arabis paniculata Franch

作　　者：罗茜 方正[1] 余婕 翁庆北[1,2] 朱斌 Luo Xi;Fang Zheng;Yu Jie;Weng Qingbei;Zhu Bin(School of Life Science,Guizhou Normal University,Guiyang,550025;Qiannan Normal University for Nationalities,Duyun,558000)

机构地区：[1]贵州师范大学生命科学学院,贵阳550025 [2]黔南民族师范学院,都匀558000

出　　处：《分子植物育种》2022年第7期2261-2270,共10页Molecular Plant Breeding

基　　金：贵州省科技计划项目(黔科合平台人才[2019]5617号);贵州省优秀青年科技人才项目(黔科合平台人才[2019]5655号)共同资助。

摘　　要：为探究圆锥南芥(Arabis paniculata Franch)叶绿体基因组特征及密码子使用偏好性,本研究利用MISA、CUSP和CodonW等软件对圆锥南芥的叶绿体基因组的SSR位点、系统发育及密码子偏好性进行分析。研究结果表明,圆锥南芥的完整叶绿体基因组长度为153541 bp,基因组平均GC含量为36.41%,其IR、LSC及SSC区长度分别26419 bp、82679 bp及18024 bp。注释得到128个基因,包括85个蛋白编码基因,35个tRNA基因和8个核糖体rRNA基因。SSR分析共发现67个SSR位点,绝大多数属于单碱基重复的A/T类型。系统进化分析表明,圆锥南芥与所选的两个南芥属物种遗传距离较远,单独聚为一支。密码子偏好性分析显示,圆锥南芥叶绿体基因组密码子使用模式主要受到自然选择和突变双重因素的影响,共筛选出22个最优密码子,其中21个(95.45%)以A/U结尾。本研究可为圆锥南芥系统发育、叶绿体基因组密码子优化、外源基因表达效率以及进一步的遗传改良和育种相关研究提供参考依据。To explore the features and codon use of Arabis paniculata Franch chloroplast(cp)genome,the MISA、CUSP and CodonW software were employed to analyze the codon usage bias of the cp genomes protein-coding sequence in Arabis paniculata in this study.The results showed that the length of the complete cp genome was153541 bp,and the average GC content was 36.41%,among which the IR,SSC and LSC regions were 26419 bp,18024 bp and 82679 bp.A total of 128 genes were identified in this cp genome,comprising of 85 protein-coding genes,35 tRNAs and 8 rRNAs.And 67 simple sequence repeats(SSRs)were also identified,most of which were biased towards A/T mononucleotide.Phylogenetic analysis showed that the genetic distance between A.paniculata and other Arabis was far,and it was isolated into a single branch.The codon bias analysis showed that the codon bias in A.paniculata cp genes was influenced by natural selection and mutation.A total of 22 optimal codons were selected,21(95.45%)of which ended in A/U.This study can provide the reference basis for phylogenetic development,codon optimization of chloroplast genome,exogenous gene expression efficiency,and further genetic improvement and breeding related researches.

关 键 词：圆锥南芥 叶绿体基因组 密码子偏好性 

分 类 号：Q943[生物学—植物学]