茶叶科学2024，Vol.44Issue(3)：411-430,20.
茶树大面白叶绿体基因组特征、密码子偏好性及其系统发育分析
Genomic Characteristics,Codon Preference,and Phylogenetic Analysis of Chloroplasts of Camellia sinensis cv.'Damianbai'
摘要
Abstract
'Damianbai'was approved as a national tea cultivar by the National Crop Variety Approval Committee in 1985,but its origin and evolutionary relationship with other tea resources are still unclear.Using'Damianbai'as the experimental material,high-throughput sequencing technology was used to sequence,assemble and annotate the entire chloroplast genome of'Damianbai'.In order to provide a basis for studying its phylogenetic evolutionary relationship,bioinformatics software was used to analyze the characteristics,phylogeny,and codon preference of its chloroplast genome.The results show that the chloroplast genome of the tea cultivar'Damianbai'had a total length of 157 129 bp and was a typical tetrad structure,including 1 LSC region(86 687 bp),1 SSC region(18 282 bp),and 2 IR regions(including IRa and IRb,both of which were 26 080 bp).A total of 135 functional genes were annotated in the chloroplast genome of'Damianbai',including 90 CDS genes,8 rRNA genes,and 37 tRNA genes.A total of 52 SSRs and 50 Longrepeat sequences were detected in the chloroplast genome of'Damianbai'.The SSRs had only A/T single nucleotide repeat sequences,while Longrepeat sequences had only two types:forward repeat and palindrome repeat.The codon usage bias in the chloroplast genome of tea cultivar'Damianbai'was mainly influenced by natural selection,and was less affected by internal mutation pressure.The chloroplast gene of tea cultivar'Damianbai'had 14 optimal codons(AAU,GAU,UGU,AAA,UAA,GCA,GCU,GGU,CCU,GUA,CGU,CUU,AGU,UCU).The Camellia sinensis cv.'Damianbai'had a close genetic relationship with Camellia sinensis isolate Baiyin cultivar Phoenix Dancong Tea(OL690374).This study analyzed the chloroplast genome sequence characteristics and phylogenetic relationships of'Damianbai',which provided a reference basis for strengthening the identification of tea cultivar'Damianbai'and the development and utilization of its resource diversity.关键词
茶树大面白/叶绿体基因组/序列特征/密码子偏好性/最优密码子/系统发育分析Key words
Camellia sinensis cv.'Damianbai'/chloroplast genome/sequence characteristics/codon usage bias/optimal codons/phylogenetic analysis分类
农业科技引用本文复制引用
尹明华,张嘉欣,乐芸,何凡凡,黄添慧,张牧彤..茶树大面白叶绿体基因组特征、密码子偏好性及其系统发育分析[J].茶叶科学,2024,44(3):411-430,20.基金项目
国家自然科学基金项目(31960079、31860084、32060092),江西省现代农业产业技术体系建设专项(JXARS-13-赣东站),2022年上饶市科技专项项目(饶科发[2023]5号社发类,2022A008) （31960079、31860084、32060092）
