厚壳红瘤果茶叶绿体基因组特征及密码子偏好性分析  

Analysis on Chloroplast Genome Characteristics and Codon Usage Biases of Camellia rubituberculata

作　　者：肖旭 赵紫涵 陆江桃 杨国园 李志 XIAO Xu;ZHAO Zihan;LU Jiangtao;YANG Guoyuan;LI Zhi(College of Forestry,Guizhou University,Guiyang 550025,China)

机构地区：[1]贵州大学林学院,贵阳550025

出　　处：《种子》2022年第12期19-26,共8页Seed

基　　金：贵州省科技计划项目(黔科合基础-ZK[2022]一般072);贵州大学引进人才项目(贵大人基合字[2019]59号)。

摘　　要：为探究厚壳红瘤果茶的叶绿体基因组功能结构及密码子使用偏好性,利用CodonW、CUSP和CHIP等软件筛选出了57条蛋白编码序列,进行中性绘图分析、ENC-plot和PR 2-plot分析。结果表明,厚壳红瘤果茶叶绿体基因组全长157044 bp,呈四段式结构,序列已登记GenBank(MN 913340);注释得到136个基因,其中包括83个蛋白编码基因,45个tRNA基因和8个rRNA基因。GC平均含量为38.04%,有效密码子数量在35.64~56.67之间,平均值为46.44,密码子偏好性较弱;且RSCU>1的32个密码子中,有28个密码子以A或U碱基结尾,证明叶绿体基因组偏好使用A或U结尾的密码子;中性绘图分析、ENC-plot分析以及PR 2-plot偏倚分析结果都证明,自然选择是密码子偏好性的重要影响因素,且筛选得到12个最优密码子(UUG、UCU、UCC、UCA、CCC、CCA、ACC、ACA、AGG、GAU、GGA、AUA)。本研究为在分子水平上研究山茶属植物的系统进化提供了相应的数据支持。In order to explore the functional structure of chloroplast genome and the codon usage preference of the tea Camellia rubituberculata,57 protein coding sequences were screened by CodonW,CUSP and CHIP,and then analyzed by neutral mapping,ENC-plot and PR 2-plot.The results showed that the total length of chloroplast genome was 157044 bp,showing a four-segment structure,and the sequence was GenBank(MN 913340).A total of 136 genes were obtained,including 83 protein-coding genes,45 tRNA genes and 8 rRNA genes.The average content of GC was 38.04%,and the number of effective codons ranged from 35.64 to 56.67,with an average value of 46.44,indicating weak codon bias.Among 32 codons with RSCU>1,28 codons ended in A or U,indicating that the chloroplast genome preferred to use codons ending in A or U.The results of neutral plot analysis,ENC-plot analysis and PR 2-plot bias analysis all proved that natural selection was an important factor influencing codon bias,and 12 optimal codons(UUG,UCU,UCC,UCA,CCC,CCA,ACC,ACA,AGG,GAU,GGA,AUA)were screened.This study provided relevant data support for studying the phylogeny of Camellia plant at the molecular level.

关 键 词：厚壳红瘤果茶 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：S685.14[农业科学—观赏园艺]