米槠叶绿体基因组密码子偏好性分析
Analysis of Codon Bias in Chloroplast Genome of Castanopsis carlesii
江淑珍 1连辉 2熊远芳 1张赛 1陈世品1
作者信息
- 1. 福建农林大学林学院,福州,350002;福建农林大学园林学院,国家林业和草原局兰花保护与利用重点实验室,福州,350002
- 2. 福建农林大学林学院,福州,350002
- 折叠
摘要
利用CodonW 1.4.2和在线软件CUSP分析米槠叶绿体基因组密码子的偏好性,并将筛选出的50条叶绿体基因组基因分成7类.结果显示,米槠叶绿体基因组密码子第3位GC平均含量为29.03％,有31个密码子RSCU值大于1,其中29个以A或U为结尾,表明该物种密码子偏好以A或U结尾.ENC范围为38.42～56.53,平均值为48.05,CAI平均值为0.168,说明密码子使用偏好性低.中性绘图分析、ENC-plot分析和PR2-plot偏倚分析均表明,选择压力是影响密码子偏好性的主要因素.有12个最优密码子被筛选出来,其中9个以U或A结尾.利用CDS序列构建的系统演化树和用RSCU值构建的聚类树状图有部分一致,表明密码子偏好性与物种进化关系有关.
Abstract
Codon bias of chloroplast genome in Castanopsis carlesii was analyzed by CodonW 1.4.2 and online software CUSP,and 50 chloroplast genome genes were screened and divided into 7 classes.The results showed that the average GC content of the third codon in the chloroplast genome of C.carlesii was 29.03％,and 31 codon RSCU values were greater than 1,of which 29 codon ended in A or U,indicating that this species preferred to end in A or U.The ENC range was 38.42 to 56.53,the mean value was 48.05,and the CAI mean value was 0.168,indicating a low codon usage bias.Neutral plot analysis,ENC-plot analysis and PR2-plot bias analysis all showed that selection pressure was the main factor affecting codon preference.Twelve optimal codons were select-ed,nine of which ended in U or A.The phylogenetic tree constructed by CDS sequence and the cluster tree con-structed by RSCU value have some similarities,indicating that codon preference is related to the evolutionary rela-tionship of species.
关键词
米槠(Castanopsis/carlesii)/叶绿体基因组/密码子偏好性/系统发育分析Key words
Castanopsis carlesii/Chloroplast genome/Codon usage bias/Phylogenetic analysis引用本文复制引用
基金项目
福建农林大学科技创新专项(118/KF2015088)
福建农林大学林学高峰学科建设项目(71201800708)
出版年
2024
NETL
NSTL
万方数据