阳春砂叶绿体全基因组解析及系统发育研究

以姜科(Zingiberaceae)豆蔻属(Amomum Roxb.)阳春砂(Amomum villosum)为试材,利用Illumina Hiseq 4000测序平台对阳春砂叶绿体基因组进行测序,通过生物信息学分析方法进行序列组装、注释和特征分析,以揭示阳春砂与其他姜科植物的进化关系及其在系统发育中的地位,为豆蔻属植物的物种鉴定提供理论依据。结果表明:(1)阳春砂叶绿体基因组全长164 069 bp,GC含量为36.1%,包括1对29 959 bp的反向重复区(IR)、一个大单拷贝区(LSC;88 798 bp)和一个小单拷贝区(SSC;15 353 bp);共注释得到133个基因,包括8个rRNA基因、38个tRNA基因和87个蛋白编码基因。(2)在阳春砂基因组中共检测到157个SSR位点,大部分SSR均由A和T组成;豆蔻属物种在基因组大小、IR边界区高度保守,核酸变异主要发生在LSC和SSC区。(3)最大似然法(Maximum Likelihood, ML)聚类分析显示,阳春砂与同属的爪哇白豆蔻(Amomum compactum)和白豆蔻(Amomum kravanh)亲缘关系最近,并且与山姜属(Alpinia Roxb.)也有较近的亲缘关系。

Complete Chloroplast Genome and Phylogenetic Analysis of Amomum villosum

With Amomum villosum (genus Amomum, family Zingiberaceae) as material, we obtained the complete chloroplast genome sequence using Illumina Hiseq 4000 sequencing platform, and then assembled, annotated, and characterized by bioinformatic methods. This study clarified the genetic relationship among species of Zingiberaceae, and provided scientific basis for the study of phylogeny and species identification of genus Amomum. The results showed that: (1) the total length of chloroplast genome was 164 069 bp and the GC content was 36.1%, including a pair of 29 959 bp reverse repeat region (IR), a large single copy region (LSC; 88 798 bp) and a small single copy region (SSC; 15 353 bp). A total of 133 genes were annotated, including 8 rRNA genes, 38 tRNA genes and 87 protein coding genes. (2) 157 SSR loci were detected in the A. villosum genome, and most of the SSR was composed of A and T. The cp genome size and IR boundary of genus Amomum were highly conserved, while nucleotide variability mainly occurred in LSC and SSC regions. (3) The maximum likelihood method (ML) cluster analysis showed that A. villosum had the closest genetic relationship with A. compactum and A. krervanh, and had a close relationship with genus Alpinia.