珍稀濒危植物越南小花金花茶的叶绿体基因组特征分析

Analysis of chloroplast genome features of endangered and rare plant Camellia minima

关键词:  越南小花金花茶, 叶绿体基因组, 特征分析, 系统发育分析, 密码子偏好性

Key words:  Camellia minima, chloroplast genome, characteristic analysis, phylogenetic analysis, codon preference

摘要:

越南小花金花茶(Camellia minima)是一种珍稀濒危的金花茶组植物,目前尚未有其叶绿体基因组的相关研究。该研究利用Illumina HiSeq 2000平台对越南小花金花茶进行了叶绿体基因组序列的测序、组装、注释和分析。结果表明:(1)越南小花金花茶叶绿体基因组全长156 961 bp,为典型的四分体结构,共注释到136个基因,其中包含87个蛋白编码基因、41个tRNA基因和8个rRNA基因。(2)分析鉴定出66个SSR位点和39个重复序列。(3)密码子偏好使用以A/U结尾的密码子,综合有效密码数(ENC)绘图、PR2-plot和中性分析推测自然选择是影响密码子使用模式的主导因素。(4)边界分析显示ycf1基因的长度和位置在不同金花茶组植物间存在差异。(5)对已发表的金花茶组植物叶绿体基因组的系统发育分析发现越南小花金花茶与小花金花茶聚为一支,亲缘关系最近。该研究结果为探索物种进化和提高外源基因表达提供了重要的参考信息,同时为后续的金花茶组植物的保护和利用提供了理论基础。

Abstract:

Camellia minima, a rare and endangered species of sect. Chrysantha, has not been previously explored in terms of its chloroplast genome. Utilizing the Illumina HiSeq 2000 platform, the chloroplast genome sequence of C. minima was sequenced, assembled, annotated, and analysed. The results were as follows:(1)The chloroplast genome of C. minima was 156 961 bp in length, embodied a typical tetrad structure, and contained 136 annotated genes, including 87 protein-coding genes, 41 tRNA genes, and 8 rRNA genes.(2)The analysis identified 66 SSR loci and 39 repetitive sequences.(3)Codons prefered to use codons ending in A/U. Comprehensive effective number of codons(ENC)mapping, PR2-plot, and neutral analyses suggested natural selection as a primary factor shaping codon usage patterns.(4)Boundary analysis showed variation in the length and position of the ycf1 gene among different species of yellow Camellia.(5)Phylogenetic analysis of the chloroplast genomes of published sect. Chrysantha species revealed that C. minima was most closely related to C. micrantha. This study provides crucial references for exploring species evolution and enhancing exogenous gene expression, establishing a theoretical foundation for the conservation and utilization of species of sect. Chrysantha in the future.