18种苔藓植物rbcL基因的密码子偏性及聚类分析  

Cluster analysis and codon usage bias studies of rbcL genes in 18 Bryophytes

作　　者：张家榕[1] 雷万钧[1] Zhang Jiarong;Lei Wanjun(College of Life Sciences,Shanxi Agricultural University,Taigu 030801,China)

机构地区：[1]山西农业大学生命科学学院,山西太谷030801

出　　处：《山西农业大学学报（自然科学版）》2020年第6期1-12,共12页Journal of Shanxi Agricultural University(Natural Science Edition)

摘　　要：[目的]以18种具有代表性的苔藓植物的叶绿体rbcL基因为研究对象,利用生物信息学方法探究其碱基组成及密码子使用特征,并用不同方法进行聚类分析。[方法]运用密码子偏性分析软件Codon W 1.4.2、碱基组成分析软件DNA star及EMBOSS的CUSP程序探究18种苔藓植物的密码子使用特征,用EBI的Clustal W模块和SPSS分别基于蛋白编码区(Codoning DNA sequence,CDS)核酸序列和同义密码子相对使用度(relative synonymous codon usage,RSCU)进行聚类分析。[结果]各物种rbcL基因AT含量较高;RSCU>1的密码子多以A/T结尾;18种苔藓植物之间氨基酸对密码子的选择具有较强的相似性;聚类分析中,基于CDS核酸序列的聚类基本反应真实的系统发育分类,而基于RSCU的聚类与其不一致。[结论]rbcL基因偏好使用以A/T结尾的密码子,本文分析的18种苔藓植物在进化上具有较近的进化关系,但基于CDS核酸序列的聚类和基于RSCU的聚类结果不一致,可能是由于进化过程中个别基因发生了突变。[Objective]The chloroplast rbcL genes of 18 Bryophytes were used as the research object.To explore their base composition and codon usage characteristics using bioinformatics methods.[Methods]In this study,we used various software including Codon W,DNA star,and CUSP programs to investigate the codon usage characteristics of 18 Bryophytes.Clustal W and SPSS were used to cluster the genes based on Codoning DNA sequence(CDS)and relative synonymous codon usage(RSCU),respectively.[Results]AT content of rbcL gene was high in all species;the codons of RSCU>1 mostly ended with A/T;The choice of codons for amino acids among 18 species of bryophytes had strong similarity.In cluster analysis,the clustering based on CDS nucleic acid sequence basically reflected the real phylogenetic classification,while RSCU-based clustering was inconsistent with it.[Conclusion]The rbcL gene prefers to use codons ending with A or T in dicots.The 18 species of Bryophytes analyzed in this study have a close evolutionary relationship,but the results of clustering based on the CDS nucleic acid sequence and the clustering based on RSCU were inconsistent,which may be due to individual genes having the mutation during the evolutionary process.

关 键 词：RBCL基因 苔藓植物 密码子使用偏好 聚类分析 

分 类 号：Q943[生物学—植物学]