薯蓣和叉蕊薯蓣叶绿体基因组及特异性DNA条形码鉴定序列筛选研究  

Complete chloroplast genomes of Dioscorea opposite and D. collettii and screening specific DNA barcodes

作　　者：马双姣 周建国[1] 李滢[1] 陈新连 吴明丽 孙伟[3] 李永华 宋经元[1] 姚辉[1] MA ShuangJiao;ZHOU JianGuo;LI Ying;CHEN XinLian;WU MingLi;SUN Wei;LI YongHua;SONG JingYuan;YAO Hui(Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People ＇s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences ＆ Peking Union Medical College, Beijing 100193, China;Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China;Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;Department of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001, China)

机构地区：[1]中国医学科学院北京协和医学院药用植物研究所,国家中医药管理局中药资源保护重点研究室,北京100193 [2]湖北中医药大学药学院,武汉430065 [3]中国中医科学院中药研究所,北京100700 [4]广西中医药大学药学院,南宁530001

出　　处：《中国科学：生命科学》2018年第5期571-582,共12页Scientia Sinica(Vitae)

基　　金：国家科技支撑计划(批准号：2011BAI07B08); 中国医学科学院医学与健康科技创新工程项目(批准号：2016-I2M-3-016)资助

摘　　要：前期研究表明,目前常用的DNA条形码序列对薯蓣属物种的鉴定效率低.本研究利用高通量测序技术测定了薯蓣(Dioscorea opposita)和叉蕊薯蓣(D.collettii)叶绿体基因组,完成了其物理图谱绘制,基因组结构特征解析,特异性DNA条形码序列的筛选.薯蓣和叉蕊薯蓣叶绿体基因组总长度分别为152963和153870 bp,均包含两个反向重复区(IRs)、一个大单拷贝区(LSC)和一个小单拷贝区(SSC)4部分.薯蓣和叉蕊薯蓣均含有125个基因,其中包含87个蛋白编码基因、30个t RNA和8个r RNA.薯蓣和叉蕊薯蓣的GC含量分别为37.04%和37.17%,经多序列比对发现薯蓣属叶绿体基因组中非编码区变异高于保守的蛋白编码区域,LSC区、SSC区变异大于IR区,筛选出了10个潜在的适合作为鉴定薯蓣属植物的特异性DNA条形码序列,其中包括5个蛋白编码基因和5个基因间隔区.系统进化树显示,叶绿体全基因组序列也可作为薯蓣属物种鉴定的超级条形码.本研究为薯蓣属系统进化以及物种鉴定等领域的研究提供依据.Previous studies of DNA barcoding Dioscorea species have shown that the identification efficiency was low. In this study, the complete chloroplast genomes of D. opposite and D. collettii were sequenced using Illumina Hi Seq 2000. Genome structure and content and high variation regions were analyzed. The complete chloroplast genome lengths of D. opposite and D. collettii were152963 and 153870 bp, which include four parts： two inverted repeats（IRs）, one large single copy（LSC） and one small single copy（SSC）. Both of D. opposite and D. collettii encoded 125 genes, including 87 protein coding genes, 30 t RNA genes and eight r RNA genes. The GC contents of D. opposite and D. collettii were 37.04% and 37.17%, respectively. The result showed that the sequence variation of non-coding regions is higher than that of the protein coding region and the variations of the LSC and SSC are higher than that of the IRs. Ten molecular markers of Dioscorea, which include five protein coding regions and five non-coding regions were screened to be used as the potential DNA barcodes for authenticating Dioscorea species. Phylogenetic analyses showed that the chloroplast genome can be used as an ultra-barcode to distinguish Dioscorea species from each other. This study laid the foundation for super barcode utilization in the Dioscorea and provided a molecular basis for further investigation on this important medicinal species.

关 键 词：薯蓣 叉蕊薯蓣 叶绿体基因组 DNA条形码 鉴定 

分 类 号：Q943.2[生物学—植物学]