摘要
密码子偏好性（codon usage bais, CUB）是指生物体中编码同一种氨基酸的同义密码子的非均衡使用现象。本研究以35对引物获得的马尾松叶绿体全基因组为研究对象,利用CodonW、CAT1.3、EMBOSS等软件对马尾松叶绿体基因组中45条编码序列（coding sequences, CDS）进行了CUB分析,并将之与火炬松、北美鹅掌楸、杉木、雪松以及拟南芥等的叶绿体基因组CUB进行比较分析。分析显示,参试物种的叶绿体基因组都偏好以AT碱基结尾的密码子,且不同物种的CUB的偏性程度不同;中性绘图分析、ENC-plot以及PR2-plot偏倚分析等均表明：马尾松叶绿体基因组CUB在密码子第三位点上A/G的使用频率较高,且受到了选择等因素的影响;利用叶绿体基因密码子RSCU值对参试物种进行聚类分析发现,亲缘关系较近的马尾松与火炬松、雪松聚为一类,三者具有类似的密码子使用模式,也说明叶绿体密码子偏好性与亲缘关系存在一定的相关性。因此,叶绿体基因组CUB研究可以为系统进化的相关研究提供相关依据。
Codon Usage Bais （CUB） refers to the non-equilibrium use of synonymous codons encoding the same amino acid. In this study, The CUB analysis of 45 Coding Sequences （CDS） in the chloroplast genome （CPG） of Pinus massoniana amplified by 35 primers were carried out using CodonW, CAT1.3, EMBOSS, etc. In addition, CUBs of CPG were compared with Pinus taeda, Liriodendron tulipifera, Cunninghamia lanceolate, Cedrus deodara and A rab- idopsis thaliana. The results showed that the CPGs of the tested species preferred the codons of the NNA and NNT and have different levels of CUB. Neutral-plot, ENC-plot and PR2-plot bias analysis showed that the frequency of A/G ofP. massoniana chloroplast genome was higher in the third place of codon, and natural selection play an imp- ortant role in formation of CUBs. The analysis of cluster was conducted based on the RSCU and showed that P. ma- ssoniana, P. taeda and Cedrus deodara have similar CUBs which indicate CUBs have a correlation with genetic re- lationship in some degrees. Therefore, the study of CUBs in chloroplast genome can be useful in phylogenetic analysis.
作者
叶友菊
倪州献
白天道
徐立安
Ye Youju;Ni Zhouxian;Bai Tiandao;Xu Lian(The Key Laboratory of Forest Genetics and Gene Engineering,Nanjing Forestry University,Nanjing,210037;Forestry College of Guangxi Univer-sity,Nanning,530004)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2018年第10期4464-4471,共8页
Genomics and Applied Biology
基金
国家自然科学基因金项目(31400575)
福建省林木种苗科技攻关项目
江苏高校优势学科项目(PAPD)共同资助
关键词
马尾松
叶绿体基因组
密码子偏好性
选择
Pinus massoniana
Chloroplast genome
Codon preference
Selection
