摘要
辣椒(Capsicum L.)属于重要的蔬菜和香料作物,在世界范围广泛栽培。种质资源是育种和生产的基础,开展辣椒属叶绿体基因组特征研究对阐明辣椒种质资源遗传多样性、培育和改良栽培品种具有重要的理论和实践价值。本研究从NCBI数据库下载13个辣椒属物种叶绿体基因组序列,利用REPuter、MISA和mVISTA等软件,对辣椒属叶绿体基因组特征、序列重复、结构变异和系统发育进行分析。结果显示:辣椒属叶绿体基因组均具有保守的四分体结构,一对反向重复区(IRs)将大单拷贝区(LSC)和小单拷贝区(SSC)分开,基因组全长介于156583~158077 bp之间,包含113个unique基因,其中蛋白编码基因、tRNA基因和rRNA基因数分别为79、30和4;含有60~127对长重复序列,其中正向重复序列和回文重复序列比例较高,30~39 bp的重复序列含量较高;发现150~164个SSR位点,以单核苷酸和二核苷酸重复为主,多为A或T碱基重复;基因组序列同源性较高,未发现基因重排现象,非编码区序列变异高于基因编码区,LSC和SSC的多样性位点多于IR;发现rps18-rpl20、rps4-trnT、ndhF-rpl32-trnL和ycf1等4个核苷酸多态性热点,LSC和SSC的序列多样性高于IR;主要栽培种辣椒(C.annuum)与多花辣椒(C.tovarii)亲缘关系较近,中华辣椒(C.chinense)与灌木状辣椒(C.frutescens)和紫绿花辣椒(C.eximium)亲缘关系较近。研究中筛选的SSR和核苷酸多态性热点可作为辣椒属物种鉴定和遗传多样性分析的分子标记,研究明确了辣椒属物种的系统发育关系,为辣椒属物种遗传多样性和生物育种奠定基础。
Pepper(Capsicum spp.)is widely used as food,spice,decoration,and medicine.Multiple cultivated Capsicum species belong to important vegetable and spice crops.The analysis of the chloroplast genome of Capsicum has impor-tant theoretical and practical value for clarifying the genetic diversity of Capsicum germplasm resources and cultivating and improving cultivated varieties.The availability of complete chloroplast genome sequences has offered enormous opportunity to researchers to study the details of gene number,characterization,phylogenetic relationships and diversi-fication of Capsicum species.The complete chloroplast genome sequences of 13 Capsicum species were downloaded from the NCBI database,and analyzed by online softwares,such as REPuter,MISA,and mVISTA.The chloroplast ge-nome of Capsicum had a conserved quadripartite structure,a pair of inverted repeats(IRs)separated a large single copy(LSC)region and a small single copy(SSC)region.The size of chloroplast genome sequences ranged from 156583 bp(C.lycianthoides)-158077 bp(C.frutescens).A total of 113 unique genes were predicted,including 79 protein-coding genes,30 tRNA genes,and four rRNA genes.About 60-127 pairs of repeats were identified in Capsicum chloroplast genomes,and the proportion of forward repeats and palindromic repeats and 30-39 bp repeats were all high in the chloroplast genomes.About 150-164 potential SSRs were reported in Capsicum chloroplast genomes,and SSRs mainly consisted of mononucleotide and dinucleotide repeats,and most of the repeats were composed of A or T base.Compara-tive genomics of the 13 Capsicum species revealed a high sequence similarity in genome-wide organization and a lower sequence divergence in the IRs than LSC and SSC.The fragments of rps18-rpl20,rps4-trnT,ndhF-rpl32-trnL and ycf1 were identified as variable regions in Capsicum species,and the nucleotide variability of LSC and SSC was higher than that of IR.The phylogenetic analysis showed that the main cultivated species C.annuum was closely related to C.tovarii,and C.chinense was closely related to C.frutescens and C.eximium.The SSR and variable hotspots identified could be used as molecular markers for species identification and genetic diversity analysis of Capsicum species.Over-all,our study would highlight the taxonomic utility of the chloroplast genomes in Capsicum species,and lay a founda-tion for the evolution,genetic diversity,conservation and biological breeding of Capsicum species.
作者
刘潮
韩利红
代小波
刘宸语
LIU Chao;HAN Lihong;DAI Xiaobo;LIU Chenyu(Yunnan Engineering Research Center of Fruit Wine,College of Biological Resource and Food Engineering,Qujing Normal Univer�sity,Qujing,Yunnan 655011,China)
出处
《热带作物学报》
CSCD
北大核心
2022年第3期447-454,共8页
Chinese Journal of Tropical Crops
基金
国家自然科学基金项目(No.32060710,No.31860005)。
