紫菜薹叶绿体全基因组序列及其系统发育分析  

Chloroplast Genome Sequence and Phylogenetic Analysis of Brassica rapa var.purpuraria

作　　者：王传之 周贤玉 李扬眉 肖婉钰 王雨凤 任海龙 WANG Chuanzhi;ZHOU Xianyu;LI Yangmei;XIAO Wanyu;WANG Yufeng;REN Hailong(School of Biology and Food Engineering,Suzhou University,Suzhou Anhui 234000,China;Guangzhou Institute of Agricultural Science,Guangzhou 510308,China;Institute of Crop Research,Guangdong Academy of Agricultural Sciences/Key Laboratory of Crop Genetic Improvement of Guangdong Province,Guangzhou 510640,China)

机构地区：[1]宿州学院生物与食品工程学院,安徽宿州234000 [2]广州市农业科学研究院,广州510308 [3]广东省农业科学院作物研究所/广东省农作物遗传改良重点实验室,广州510640

出　　处：《西北农业学报》2024年第8期1483-1494,共12页Acta Agriculturae Boreali-occidentalis Sinica

基　　金：宿州学院国家级大学生创新创业训练计划(202310379012);宿州学院博士(后)科研启动基金(2023BSK022);宿州学院分子育种中心横向课题(2022xhx235,2023xhx129);安徽省教育厅重点项目(2022AH051384)。

摘　　要：紫菜薹(Brassica rapa var.purpuraria)是十字花科芸薹属白菜亚种中的一个变种,通过Illumina高通量测序平台,对其叶绿体基因组进行测序、组装和注释。结果表明,紫菜薹叶绿体基因组为典型的四分环状结构,大小为153483 bp,GC含量为36.36%,由长度为83282 bp的大单拷贝区(LSC)、17775 bp的小单拷贝区(SSC)和1对各26213 bp的反向重复区(IRa/IRb)组成。基因组注释共得到132个基因,包括:87个蛋白编码基因,37个tRNA和8个rRNA。共鉴定到313个简单重复序列(SSR)和37个散在重复序列。密码子偏好性分析发现存在偏好使用A/U碱基结尾的现象。边界分析和序列变异分析显示,芸薹属叶绿体基因组非常保守,其中SSC区差异性最大,变异程度最高,IR区差异性最小,最为保守。基于叶绿体基因组序列的系统发育分析表明,紫菜薹在分类上与白菜的其他变种在一个小分支中。研究结果可为芸薹属植物,特别是白菜种的分类学、系统学和生物地理学研究提供参考。Zicaitai(Brassica rapa var.purpuraria)is a variety of Brassica rapa subspecies belonging to the Brassicaceae family.The chloroplast genome of Brassica rapa var.purpuraria was sequenced,assembled,and annotated using the Illumina high-throughput sequencing platform.The results indicated that the chloroplast genome of Brassica rapa var.purpuraria had a typical quartered circular structure,with a size of 153483 bp and GC content of 36.36%.It comprises a large single copy region(LSC)of 83282 bp,a small single copy region(SSC)of 17775 bp,and a pair of reverse repeat regions(IRa/IRb)of 2×26213 bp.Genome annotation predicted 132 genes,including 87 protein coding genes,37 tRNAs,and 8 rRNAs.Additionally,313 simple repeat sequences(SSRs)and 37 scattered repeat sequences were identified.Codon bias analysis found that there was a bias for using A/U base endings.Boundary analysis and sequence variation analysis demonstrated the chloroplast genome of Brassica to be highly conservative,SSC region of chloroplast genome had the largest difference and the highest degree of variation,while the IR region had the smallest difference and was the most conservative.Phylogenetic analysis based on the chloroplast genome sequence indicated that Brassica rapa var.purpuraria belongs to the same branch as other varieties of Brassica rapa.This study provides a reference for the taxonomic,systematic,and biogeographical studies of Brassica genus,particularly Brassica rapa species.

关 键 词：白菜 紫菜薹 叶绿体基因组 系统发育分析 

分 类 号：S63[农业科学—蔬菜学]