ABSTRACT
ObjectiveThe transcriptome characteristics of different tissues of Codonopsis pilosula were analyzed to illustrate the genetic basis of the accumulation of active ingredients in the root of C. pilosula， and to provide theoretical basis for its high-quality production and cultivation. MethodDifferent tissues of C. pilosula at flowering stage were selected as experimental materials， and the contents of tangshenoside Ⅰ， lobetyolin and atractylenolide Ⅲ were detected by high performance liquid chromatography（HPLC）. RNA-Seq was used to perform transcriptome sequencing of different tissues， and the differentially expressed genes were screened and analyzed by Gene Ontology（GO） and Kyoto Gene and Encyclopedia of Genes and Genomes（KEGG） enrichment analysis， in order to explore the characteristics of active compound distribution and the transcriptional profiles. ResultThe contents of polysaccharides and tangshenoside Ⅰ in the root of C. pilosula were significantly higher than those in other tissues. The transcriptional profiles of the root were significantly different from those of stem， leaf and flower. Cluster analysis， GO and KEGG enrichment analysis of differential gene expression showed that the differential expression genes were mainly enriched in flavonoid and phenylpropanoid biosynthesis， sucrose-starch metabolism， plant hormone signal transduction， plant-pathogen interaction， mitogen-activated protein kinase（MAPK） cascade signal transduction， Adenosine triphosphate（ATP）-binding cassette（ABC） transporter and other pathways. The expression of genes related to biosynthesis of phenylpropanoid compounds were significantly up-regulated in the roots and flowers， and ABC transporter proteins were mostly highly expressed in the flowers. The expression of key enzyme genes for polysaccharide synthesis， such as sucrose：sucrose 1-fructosyltransferase（1-SST） and fructan 1-exohydrolase（1-Feh）， were significantly up-regulated in the roots， and a large number of stress-responsive genes closely related to the accumulation of secondary metabolites were significantly up-regulated in the roots. ConclusionThe active compound content and transcriptional profiles in C. pilosula roots were significantly different from those in stem， leaf， flower and other tissues， showing tissue specificity. Meanwhile， the genes related to stress response and biosynthesis of active compound， such as fructan and phenylpropanoid compounds， were up-regulated in roots of C. pilosula.