基于PacBio测序的对叶百部叶绿体基因组结构及系统发育分析  

Chloroplast Genome Structure of Stemona tuberosa and Phylogenetic Analysis Based on PacBio Sequencing

作　　者：连艳[1] 黄凤[1] 朱文涛[2] 刘晓芬[1] 吴昊 蒋桂华[1] 尹显梅 LIAN Yan;HUANG Feng;ZHU Wentao;LIU Xiaofen;WU Hao;JIANG Guihua;YIN Xianmei(Key Laboratory of Standardization of Chinese Medicine,State Key Laboratory of Southwestern Chinese Medicine Resources,School of Pharmacy,Chengdu University of Traditional Chinese Medicine,Chengdu 611137,China;Sichuan Academy of Chinese Medicine Sciences,Chengdu 610041,China)

机构地区：[1]成都中医药大学药学院/西南特色中药资源国家重点实验室,中药材标准化重点实验室,成都611137 [2]四川省中医药科学院,成都610041

出　　处：《中国实验方剂学杂志》2023年第14期123-132,共10页Chinese Journal of Experimental Traditional Medical Formulae

基　　金：国家自然科学基金项目(82173928);四川省自然科学基金项目(2022NSFSC1548);四川省中医药管理局科学技术研究专项(2021MS017);四川省省级科研院所基本科研业务费项目(2022JDKY0013)。

摘　　要：目的:获得对叶百部Stemona tuberosa高质量叶绿体基因组信息,明确其结构、序列特征,同时确定对叶百部的系统发育地位。方法:采用Illumina NovaSeq 6000和PacBio RSⅡ平台对对叶百部分别进行建库测序,利用生物信息软件将2个测序平台的数据进行混合组装和碱基校正,最终获得高质量叶绿体基因组,随后对其序列特征、重复序列、基因多样性和系统发育进行分析。结果:对叶百部叶绿体基因组大小为154379 bp,叶绿体基因组结构为典型环状四段式,1对27074 bp的反向重复区(IR),1个大小为17924 bp的小单拷贝区(SSC)和1个82307 bp的大单拷贝区(LSC),平均鸟嘌呤和肥嘧啶所占的比率(GC)含量为37.86%;共注释得到121个基因,包括30个tRNA基因,4个rRNA基因和87蛋白编码基因,其中6个tRNA基因和12个蛋白质编码基因中存在内含子;对叶百部叶绿体基因组中共发现49个长重复序列和59个单核苷酸简单重复序列(SSR);4个百部属的叶绿体基因组比较分析表明ycf1和ndhF基因具有高度多样性;基于叶绿体基因组构建的系统发育树与对叶百部目前的分类地位一致。结论:成功组装了对叶百部叶绿体高质量基因组,获得了包括对叶百部在内的4种百部属植物叶绿体基因组的结构及序列特征信息,为百部属药用植物的鉴定、进化和系统发育研究奠定基础。Objective:To obtain high-quality chloroplast genome information on Stemona tuberosa and clarify its structure,sequence features,and phylogenetic status.Method:The Illumina NovaSeq 6000 and PacBio RSⅡplatforms were used for library construction and sequencing of S.tuberosa,respectively.The data from both sequencing platforms were combined and subjected to bioinformatics analysis for genome assembly and base correction,resulting in a high-quality chloroplast genome.Subsequently,sequence features,repetitive sequences,gene diversity,and phylogeny were analyzed.Result:The chloroplast genome size of S.tuberosa was determined to be 154379 bp.The structure of the chloroplast genome followed the typical quadripartite circular form,consisting of a pair of inverted repeat regions(IRs)with a length of 27074 bp,a small singlecopy region(SSC)of 17924 bp,and a large single-copy region(LSC)of 82307 bp.The average GC content was 37.86%.A total of 121 genes were annotated,including 30 tRNA genes,four rRNA genes,and 87 proteincoding genes.Among them,six tRNA genes and 12 protein-coding genes contained introns.In the chloroplast genome of S.tuberosa,49 long repetitive sequences and 59 single-nucleotide simple sequence repeats(SSRs)were identified.Comparative analysis of chloroplast genomes among four Stemona species revealed high diversity in the ycf1 and ndhF genes.The phylogenetic tree constructed based on the chloroplast genome showed consistent classification with the current taxonomic status of S.tuberosa.Conclusion:The high-quality chloroplast genome of S.tuberosa was successfully assembled,providing valuable information on the structure and sequence features of chloroplast genomes in four Stemona species,including S.tuberosa.These findings lay a foundation for the identification,evolution,and phylogenetic studies of medicinal plants in the genus Stemona.

关 键 词：对叶百部 叶绿体基因组 PacBio测序 系统发育 

分 类 号：R284.2[医药卫生—中药学] R289[医药卫生—中医学] R287R22R2-031R33R24