摘要
该研究应用新一代测序技术Illumina HiSeq^(TM)4000在转录水平上对药用植物玄参根部进行测序,结合生物信息学方法开展基因功能注释和SSR位点搜索。通过测序,共获得65 602 036条原始序列。利用生物信息学软件拼接和组装序列,获得73 983条unigene,平均长度823 bp。序列同源性比较表明,56 389条unigene与其他物种具有不同程度的同源性。通过Swiss-Prot,GO,KEGG,COG比对注释,发现520条编码玄参次生代谢途径关键酶基因和191个相关转录因子。利用MISA软件在所有unigenes中共搜索到11 659个SSR位点,重复类型以二核苷酸为主。该研究所获得的参与次生代谢的关键基因可为研究玄参药用成分的生物合成和调控机制奠定基础,获得的大量SSR位点为后续研究玄参种质鉴定及遗传多样性研究提供参考。
To investigate the profile of gene function and search for SSR,a new technology of high-throughput Solexa/Illumina sequencing was used to generate the root transcriptome of Scrophularia ningpoensis,and 65 602 036 raw reads were obtained. Based on the bioinformatics analysis and Trinity,73 983 unigenes were obtained with an average length of 823 bp. The comparison of sequence homology in database showed that 56 389 unigenes had different degrees of homology. A total of 520 metabolic pathways related genes and 191 related transcription factors were identified by the Swiss-Prot,GO,KEGG and COG. The 11 659 SSRs were found by MISA and the highest frequency was AG/CT. In this study,we obtained numerous SSRs to provide references for the study of functional gene cloning and genetic diversity of S. ningpoensis. The key genes involved in the secondary metabolism are the basis for the study of biosynthesis and regulatory mechanism of the secondary metabolites.
出处
《中国中药杂志》
CAS
CSCD
北大核心
2017年第13期2460-2466,共7页
China Journal of Chinese Materia Medica
基金
重庆市"科技平台与基地建设"项目(cstc2014ptyjd10001)
中央本级重大增减支项目(2060302)
重庆市基本科研业务计划项目(2015cstc-jbky-01903)
重庆市基础与前沿研究计划项目(cstc2013jcyA10126)
关键词
玄参
转录组
高通量测序
萜类物质
Scrophularia ningpoensis
transcriptome
high throughput sequencing
terpenoids
