三倍体茶树‘西莲1号’叶绿体基因组特征及系统发育分析

Characterization and Phylogenetic Analysis of the Complete Chloroplast Genome of Triploid Tea Plant Xilian 1

三倍体茶树品种‘西莲1号’是桑植白茶产业发展的主推品种,与湖南现有茶树品种相比具有很强的特异性。为揭示‘西莲1号’的分类和演化地位,项目采用叶绿体(Chloroplast,cp)全基因组测序技术进行了‘西莲1号’全基因组测序,并对其所有的SSR标记进行了开发与筛选。结果表明:(1)‘西莲1号’叶绿体基因组全长为157038 bp,GC含量为37.30%,为一个四分体结构,包括1个大的单拷贝(LSC)、一个小的单拷贝(SSC)和一对反向重复序列(IR),长度分别为86612 bp、18282 bp和26072 bp。cpDNA共注释得到132个基因,其中unigenes有114个,包含80个编码基因,30个tRNA基因和4个rRNA基因。(2)共鉴定出245个简单序列重复(SSR),通过筛选有15个SSR具有较高的多态性。获得了cpDNA基因组20个氨基酸的偏好密码子,‘西莲1号’密码子偏好以A/T碱基结尾。(3)基因选择压力分析表明,与茶组其他资源相比,6个基因(accD、ndhC、petB、rpl16、rpoC1、rpoC2)可能处于正选择状态。(4)基于叶绿体基因组序列构建了基于22份茶组植物的系统发育树,聚类结果显示‘西莲1号’与其他栽培型茶树品种(Camellia sinensis var.sinensis)处于系统发育树的末端,属于进化的茶树资源类型。

Triploid Xilian 1 is the main tea varieties for the development of Sangzhi white tea industry,which has strong specificity compared with the other Hunan tea varieties.In order to reveal the classification and evolutionary status of Xilian 1,exploit the tea plant chloroplast SSR,the complete chloroplast genomes of Xilian 1 were sequenced using the Illumina Hiseq 2500 platform.The results showed that:(1)The cp genome is 157038 bp in length with an overall GC content of 37.30%,presenting a quadripartite structure comprising a large single copy(LSC,86612 bp),a small single copy(SSC,18282bp),and a pair of inverted repeats(IRs,26072 bp).The genome contains 132 genes which 114 were unigenes,including 80 protein-coding genes,30 tRNA genes,and 4 rRNA genes.(2)A total of 245 simple sequence repeats(SSRs)were identified,and 15 SSRs were highly polymorphic among 10 tea germplasm resource.The relative synonymous codon usage(RSCU)of 20 amino acids was obtained,and the Xilian 1 codon prefers to end with A/T base.(3)Gene selective pressure analysis showed that six genes(accD、ndhC、petB、rpl16、rpoC1、rpoC2)were possibly under positive selection compared with the other tea species.(4)Phylogenetic relationships showed that Xilian 1 and other cultivated tea varieties(Camellia sinensis Var.sinensis)were at the end of the phylogenetic tree,Xilian 1 belonging to the relatively evolutionary tea resource type.