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当前位置: 首页 > 文章 > 5种柏科植物叶绿体基因组密码子偏好性分析 福建农林大学学报(自然科学版) 2024,53 (2) 214-220
Position: Home > Articles > Codon bias analysis of chloroplast genomes of 5 Cupressaceae plants Journal of Fujian Agriculture and Forestry University(Natural Science Edition) 2024,53 (2) 214-220

5种柏科植物叶绿体基因组密码子偏好性分析

作  者：
黄思琦;张麒功;叶泽霖;覃兴化;汪其双;林协全;郑智位;林文锋;邹小兴
单  位：
福建农林大学林学院;福建省德化葛坑国有林场
关键词：
秃杉;柏科植物;叶绿体基因组;密码子偏好性;亲缘关系
摘  要：
[目的]通过叶绿体基因组密码子偏好性,分析5种柏科植物(秃杉、水杉、杉木、福建柏、日本柳杉)的亲缘关系,筛选出与秃杉亲缘相近者作为异种砧木,为秃杉无性繁殖与规模化生产提供理论参考.[方法]通过NCBI下载并筛选5种柏科植物的蛋白编码序列,使用CUSP、CodonW、SPSS、MAFFT等软件分析密码子偏好性形成模式,并构建聚类树和系统发育树.[结果]5种柏科植物叶绿体密码子的A/T碱基均较多,且第3位以A/T结尾为主;有效密码子数基本高于35,密码子使用偏好性总体较弱;由中性绘图分析、ENC-plot分析、PR2-plot分析可得,密码子偏好性的形成同时受自然选择、碱基突变等多种因素影响,且自然选择是主导因素;通过相对同义密码子分析和最优密码子分析确定AAA、CCA、GCU同时为秃杉、水杉、杉木与福建柏的最优密码子,无以G/C结尾的密码子;秃杉与水杉、杉木、福建柏、日本柳杉共有的最优密码子分别为9、7、11、7个,数量上差异较小;基于相对同义密码子使用度与基于蛋白编码序列构建的进化树结构相似,基于全序列和蛋白编码序列构建的系统进化树均显示秃杉与杉木的亲缘关系最为接近.[结论]叶绿体基因组密码子偏好性可用于异砧嫁接中砧木选择方法的优化,杉木与秃杉的亲缘关系相近,推荐使用杉木作为秃杉嫁接的异种砧木.
译  名：
Codon bias analysis of chloroplast genomes of 5 Cupressaceae plants
关键词：
Taiwania flousiana%Cupressaceae%chloroplast genome%codon bias%kinship
摘  要：
[Objective]Based on the codon preference of the chloroplast genome,the phylogeny of 5 Cupressaceae plants(Taiwaniaflousi-ana,Metasequoia glyptostroboides,Cunninghamia lanceolata,Fokienia hodginsii and Cryptomeria japonica)was analyzed,and those close to T.flousiana were selected as heterogeneous rootstock,providing theoretical reference for the clonal reproduction and large-scale produc-tion of T.flousiana.[Method]The CDS sequences of 5 species of Cupressaceae plants were downloaded and screened by NCBI,and their codon preference formation patterns were analyzed by softwares of CUSP,CodonW,SPSS and MAFFT,based on which cluster trees and phylogenetic trees were constructed.[Result]The chloroplast codons of the 5 Cupressaceae plants were mainly composed of A/T bases,and their third bases also tended to be ended with A/T.The number of effective codon was generally higher than 35,demonstrating weak codon usage bias.According to neutral plot analysis,ENC-plot analysis and PR2-plot analysis,the formation of codon bias was affected by multiple factors including natural selection,base mutation,etc.,among which natural selection predominated.Relative synonymous codon analysis and optimal codon analysis showed no optimal codon ended with G/C,and AAA,CCA and GCU were the optimal codons for T.flousiana,M.glyptostroboides,C.lanceolata and F.hodginsii.T.flousiana had 9,7,11 and 7 optimal codons with M.glyptostroboides,C.lanceolata,F.hodginsii and C.japonica respectively,with little difference in number.The structure of phylogenetic tree based on relative synonymous codon usage values was similar to that based on coding sequence,and based on both results above C.lanceolata was shown to be closest to T.flousiana.[Conclusion]The codon preference of chloroplast genome can be used to optimize the selection method of stock in different anvil grafting.C.lanceolata and T.flousiana are closely related,so it is recommended to use C.lanceolata as heterogeneous root-stock for T.flousiana grafting.

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