2种玉兰属植物叶绿体基因组密码子偏好性分析  

Analysis of Codon Usage Bias(CUB)in the Chloroplast Genomes of 2 Yulania species

作　　者：沈莲文 田金红 王玉昌 杨林[1,2] 亚华金 王大玮[1,2] Shen Lianwen;Tian Jinhong;Wang Yuchang;Yang Lin;Ya Huajin;Wang Dawei(Key Laboratory for Forest Genetic and Tree Improvement&Propagation in Universities of Yunnan Province,Southwest Forestry University,Kunming Yunnan 650233,China;Key Laboratory of Ministry of Education for Conservation and Utilization of Mountain Forest Resources in Southwest China,Southwest Forestry University,Kunming Yunnan 650233,China)

机构地区：[1]西南林业大学云南省高校林木遗传改良与繁育重点实验室,云南昆明650233 [2]西南林业大学西南山地森林资源保育与利用教育部重点实验室,云南昆明650233

出　　处：《西南林业大学学报（自然科学）》2023年第2期44-53,共10页Journal of Southwest Forestry University：Natural Sciences

基　　金：云南省高校林木遗传改良与繁育重点实验室开放基金(2017011)资助。

摘　　要：利用Codon W、CUSP及R语言等软件对2种玉兰属植物叶绿体基因组密码子的使用偏好性进行分析。结果表明:两者叶绿体基因组密码子的GC含量均为GC_(1)>GC_(2)>GC_(3),说明密码子第3位碱基A/U含量高。大部分有效密码子数(ENC)都在45以上,CAI平均值为0.167,说明密码子偏好性弱。ENC-plot、PR2-plot及中性绘图分析表明GC_(1)、GC_(2)与GC_(3)之间相关性不明显;且第3位碱基使用频率为T>A,G>C,说明2种玉兰属植物叶绿体基因组密码子的偏好形成受到自然选择和基因突变的共同影响,自然选择为主要影响因素。利用相对使用度(RSCU)、ENC值共筛选出30个最优密码子,大部分以A/U结尾,证明二乔玉兰和日本辛夷2种玉兰属植物叶绿体基因组密码子第3位碱基偏好A/U。This paper analyzed the codon usage in chloroplast genome of 2 Yulania species by Codon W,CUSP and R software.The results showed that the GC content of chloroplast genomes of 2 Yulania species was GC_(1)>GC_(2)>GC_(3),which indicated the content of base A/U at codon 3 was high.The effective number of codons(ENC)of CDS sequences exceeding 45 were more than 80 base pair,and the average CAI value was 0.167,which indicated weak codon bias.The results of ENC-plot,PR2-plot and neutral plot analysis showed that the correlation among GC_(1),GC_(2) and GC_(3) was not significant.And the usage frequency of the third base was T>A,G>C.It indicated that the formation of codon bias in chloroplast genome of 2 Yulania species was affected by natural selection and gene mutation cooperatively,and natural selection is the main affecting factor.According to the relative synonymous codon usage(RSCU)and ENC values,30 optimal ciphers ending in A/U were selected.It was demonstrated that the codon 3 position in the chloroplast genome of 2 species of Yulania soulangeana and Yulania kobus has an A/U preference.

关 键 词：二乔玉兰 日本辛夷 叶绿体基因组 密码子偏好性 

分 类 号：S685.15[农业科学—观赏园艺]