芝麻菜叶绿体基因组测序及系统发育关系分析  

Sequencing and Phylogenetic Relationship Analysis of Chloroplast Genome in Eruca sativa

作　　者：沈海斌[1] 卢盼玲 吴珏 刘军林 魏仕伟 张兆辉[5] Shen Haibin;Lu Panling;Wu Jue;Liu Junlin;Wei Shiwei;Zhang Zhaohui(Shanghai Key Laboratory of Protected Horticultural Technology,Horticultural Research Institute,Shanghai Academy of Agricultural Sciences,Shanghai,201403;Shanghai Fengxian District Vegetable Technology Extension Station,Shanghai,201499;Weining County Agricultural Rural Area,Guizhou,553100;Shanghai Agricultural Biological Gene Center,Shanghai,201106;Zhuanghang Integrated Experimental Station,Shanghai Academy of Agricultural Sciences,Shanghai,201415)

机构地区：[1]上海市农业科学院园艺研究所上海市设施园艺技术重点实验室,上海201403 [2]上海市奉贤区蔬菜技术推广站,上海201499 [3]威宁县农业农村局,贵州553100 [4]上海农业生物基因中心,上海201106 [5]上海市农业科学院庄行综合试验站,上海201415

出　　处：《分子植物育种》2022年第8期2495-2506,共12页Molecular Plant Breeding

基　　金：上海市绿叶蔬菜产业技术体系项目(沪农科产字[2021]第2-04号);上海科技兴农项目(沪农科推字[2019]第3-1号)共同资助。

摘　　要：芝麻菜作为重要的油料作物和食用蔬菜,在中国种类繁多,分布广泛。叶绿体基因组因具有多拷贝,结构保守等优点,常被用于比较基因组学、植物遗传资源研究和系统进化等。本研究利用高通量测序技术对不同品种芝麻菜(Eruca sativa)的叶绿体全基因组进行测序,分析了芝麻菜叶绿体基因组结构特征及系统进化关系。为芝麻菜的分类、分子标记开发和遗传资源研究提供一定理论基础。芝麻菜品种ZY和LY的全基因组大小分别为153628和153488 bp,均具有高等植物叶绿体基因组四分体结构,包括大单拷贝区(LSC;83325,83313 bp)、小单拷贝区(SSC;17789,17783 bp)和一对反向重复区(IRa/b;26257,26196 bp)。两者分别注释到112和113个单拷贝基因,其中ZY注释到78个m RAN基因和1个假基因,LY注释到79个mRNA基因,两者均注释到4个rRNA基因和30个tRNA基因。重复序列结果分析表明,ZY和LY叶绿体基因组中分别检测到55条和42条长重复序列;ZY和LY中均发现304个SSR位点,最多的是A/T核苷酸重复。比较基因组学分析结果表明,芝麻菜属和芸薹属植物叶绿体基因组高度保守,序列的种间变异高于种内,非编码区变异高于编码区。此外,种间和种内均筛选出2条核酸多样性较高的基因,分别为matK、rsp16、rpl32和rsp16。系统发育结果表明,本研究测得的2个芝麻菜品种和已发表的芝麻菜品种聚为一支(支持率为100%),芝麻菜与芸薹属植物欧洲油菜(Brassica napus)、甘蓝(Brassica oleracea)、芥菜(Brassica juncea)、芜菁(Brassica rapa)和萝卜(Raphanus sativus)亲缘关系更近。As an important oil crop and edible vegetable,arugula has a wide variety and widespread distribution in our country.The chloroplast genome is often used in comparative genomics,plant genetic resource research and system evolution because of its multiple copies and conservative structure.The chloroplast genome of Eruca sativa was assembled and sequenced,the structural characteristics and the phylogenetic relationship of the chloroplast genome were analyzed.It provides a theoretical basis for the classification,the development of molecular markers and the research of genetic resources of arugula.Results revealed that the complete genomes of ZY and LY were153628 and 153488 bp in length,and both exhibited the typical quadripartite circular structure consisting of a large single copy region(LSC,83325 and 83313 bp),a small single copy region(SSC,17789 and 17783 bp),and a pair of inverted repeat regions(IRa/b,26257 and 26196 bp),respectively.In total,112 and 113 unique genes were identified in ZY and LY respectively,among them,ZY annotated 78 m RAN genes and 1 pseudogene,and LY annotated 79 mRNA genes and both including 30 transfer RNA(tRNA)genes,and four ribosomal RNA(rRNA)genes.Analysis of repeated sequence results showed that a total of 55 and 42 long repeats that the length is more than 30 bp were detected in ZY and LY;304 SSR sites were found in both ZY and LY,the most being A/T nucleotide repeats.Comparative analyses revealed that the Eruca and Brassica Cp genome were highly conserved.The interspecific variation of sequence is higher than that of intraspecific,and the variation of non-coding region is higher than that of coding region.In addition,both two genes with high nucleic acid diversity were screened between species and within species,namely matK,rsp16 and rpl32,rsp16.The phylogenetic results show that two arugula varieties measured in this study and one published arugula varieties are clustered into one group(support rate is 100%),Eruca sativa is more closely related to Brassica napus,Brassica oleracea,Bra

关 键 词：芝麻菜(Eruca sativa) 叶绿体基因组 高通量测序 系统发育分析 

分 类 号：S649[农业科学—蔬菜学]