Applications of RNA-Seq technology on medicinal plants / 中草药

RNA-Sequencing (RNA-Seq) is a newly developed method to analyze gene function and interaction at the omics level, which is widely used in frontier field in molecular biology and other fields. In recent years, this technology has been intensively used in the research of medicinal plants, and growing number of reports are published. This paper systematically sorted out relevant literatures and summarized applications of RNA-Seq technology in functional gene discovery, gene network analysis, genetic mechanism revelation and development of molecular marker of medicinal plants. Meanwhile, according to the technical characteristics of RNA-Seq and the development needs of medicinal plant research, this article brings the future prospects regarding RNA-seq technology in Chinese medicinal materials, and intending to provide inspirations for researches on Chinese materia medica based on RNA-Seq.

EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences / 中国中药杂志

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding.