赖草属叶绿体基因组密码子偏好性分析  

Codon Bias Analysis in Chloroplast Genomes of LeymusSpecies

作　　者：刘文丽 王智勇 田春育 杨艳婷 刘倩 冯玉梅 武自念[3] 李志勇[3] LIU Wenli;WANG Zhiyong;TIAN Chunyu;YANG Yanting;LIU Qian;FENG Yumei;WU Zinian;LI Zhiyong(College of Grassland and Science,Qingdao Agricultural University,Qingdao 266109,China;Forestry and Grassland Bureau of Inner Mongolia Autonomous Region,Hohhot 010010,China;Institute of Grassland Research of CAAS,Hohhot 010010,China)

机构地区：[1]青岛农业大学草业学院,山东青岛266109 [2]内蒙古自治区林业和草原种苗总站,内蒙古呼和浩特010010 [3]中国农业科学院草原研究所,内蒙古呼和浩特010010

出　　处：《中国草地学报》2024年第2期14-23,共10页Chinese Journal of Grassland

基　　金：内蒙古自然科学基金(2022MS03073);中央级公益性科研院所基本科研业务费(Y2023PT02,1610332022001);内蒙古科技计划(2020GG0127);“科技兴蒙”重点专项(2020-科技兴蒙-草种业技术创新中心-1)。

摘　　要：以16种赖草属植物叶绿体基因组的50条基因序列为研究对象,使用密码子碱基组成分析、中性绘图分析、PR2-plot绘图分析、ENC-plot绘图分析、基因参数相关性分析和聚类分析等多种生物信息学方法分析赖草属叶绿体基因组密码子偏好性,结果表明:(1)赖草属叶绿体基因组密码子富含A和U,高频密码子也多以A/U结尾。(2)赖草属有效密码子数值在39.81~61.00之间。(3)16种赖草属植物根据聚类分析可分为两组,Leymus multicaulis、Leymus karelinii、Leymus racemosus、Leymus secalinus、Leymus ramosus、Leymus paboanus、Leymus duthiei、Leymus chinensis、Leymus arenarius为一组,Leymus coreanus、Leymus komarovii、Leymus triticoides、Leymus cinereus、Leymus condensatus、Leymus mollis、Leymus angustus为一组。综合分析表明,16种赖草属植物密码子偏好性受多种因素影响,选择作用影响较大,密码子的偏好性较弱,种间进化差异不显著,基因间偏差小。In this study,50 gene sequences from the chloroplast genomes of 16 species of Leymus were analyzed by various bioinformatics methods,such as codon base composition analysis,neutral plot analy⁃sis,PR2-plot analysis,ENC-plot analysis,gene parameter correlation analysis and cluster analysis.The results showed that:(1)The chloroplast genome codons of Leymus were rich in A and U,and the highfrequency codons were tended to end with A/U.(2)The ENC value ranged from 39.81 to 61.00.(3)According to cluster analysis,16 species of Leymus could be divided into two groups,Leymus multicaulis,Leymus karelinii,Leymus racemosus,Leymus secalinus,Leymus ramosus,Leymus paboanus,Leymus duthiei,Leymus chinensis,Leymus arenarius as one group,and Leymus coreanus,Leymus komarovii,Ley⁃mus triticoides,Leymus cinereus,Leymus condensatus,Leymus mollis,Leymus angustus as the other group.The comprehensive analysis showed that the codon bias of 16 species of Leymus was affected by many factors,selection had a greater effect,codon bias was weak,interspecific evolutionary difference was not significant,and intergenic deviation was small.

关 键 词：赖草属 叶绿体基因组 密码子偏好性 聚类分析 密码子使用模式 

分 类 号：S543.9[农业科学—作物学]