草果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 Amomum tsao-ko

目的明确草果Amomumtsao-ko叶绿体基因组结构特征及其在姜科的进化地位。方法利用IlluminaHiseq4000测序平台对草果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,并以绿苞闭鞘姜为外类群,通过MEGA6软件构建ML系统发育树,分析姜科物种间系统发育关系。结果草果叶绿体基因组全长163 648 bp,鸟嘌呤和胞嘧啶含量(guanine-cytosine content,GC)为36.0%,包括一对29 776 bp的反向重复区(IRs)、一个大单拷贝区(LSC,88 741 bp)和一个小单拷贝区(SSC,15 355 bp);共注释得到113个基因,包括4个rRNA基因、30个t RNA基因和79个蛋白编码基因;在草果叶绿体基因组中共检测到123个SSR位点,大部分SSR均由A和T组成;豆蔻属物种叶绿体基因组大小和结构相似,IR边界高度保守;聚类分析显示草果与豆蔻属的海南砂A.longiligulare、阳春砂A.villosum、绿壳砂A.villosum var. xanthioides、爪哇白豆蔻A. compactum和白豆蔻A. kravanh亲缘关系最近;适应性进化分析发现rpl20、rps11、ccsA、clpP、ycf1和ycf2 6个基因在进化过程中被正向选择。结论获得了完整的草果叶绿体基因组序列,明确了姜科物种间的亲缘关系,为研究豆蔻属植物的系统进化及物种鉴定提供科学依据。

Objective To clarify the structural characteristics of chloroplast genome in Amomum tsao-ko and its evolutionary status within the Zingiberaceae. Methods The chloroplast genome of A. tsao-ko was sequenced by Illumina Hiseq 4000 sequencing platform, and then assembled, annotated, and characterized by bioinformatic methods. The ML phylogenetic tree was constructed by MEGA6 software with Costus viridis as outgroup, and the phylogenetic relationship among Zingiberaceae species was analyzed. Results The total length of chloroplast genome was 163648 bp and the GC content was 36.0%, including a pair of 29776 bp reverse repeat region(IRs), a large single copy region(LSC;88741 bp) and a small single copy region(SSC;15355 bp). A total of 113 genes were annotated, including 4 rRNA genes, 30 tRNA genes and 79 protein coding genes. 123 SSR loci were detected in the A. tsao-ko chloroplast genome, and most of the SSR was composed of A and T. The chloroplast genomes of genus Amomum are similar in size and structure, and the IR boundary is highly conservative. The cluster analysis showed that A. tsao-ko was closely related to A. longiligulare, A. villosum, A. villosum var. xanthioides, A. compactum and A. kravanh. rpl20, rps11, ccsA, clpP, ycf1 and ycf2 are undergoing positive selection in the process of evolution. Conclusion The complete chloroplast genome sequence of A. tsao-ko was obtained in this study, which clarified the genetic relationship among species of Zingiberaceae, and provided scientific basis for the study of phylogeny and species identification of genus Amomum.