De novo transcriptome analysis to identify flavonoid biosynthesis genes in Stellera chamaejasme

Abstract

Stellera chamaejasme L. is a well-recognized traditional medicine in China and can synthesizes various secondary metabolites including a group of flavonoids. However, little is known about the molecular mechanisms underlying flavonoid biosynthesis. In this study, large-scale RNA sequencing on flower of S. chamaejasme produced a de novo transcriptome consisting of 32,216 unigenes with a N50 length of 1745bp. Among all unigenes, 21,355 unigenes were identified as putative homologs of annotated sequences in the public protein databases. Further functional classification revealed that the active genes in flower are predominately involved in metabolic process and biosynthesis of secondary metabolite pathways. A total of 19 candidate genes encoding 11 structural enzymes involved in flavonoid biosynthesis were identified in the unigene dataset by targeted searches of their annotations. In addition, a number of regulatory genes including MYB, basic helix-loop-helix (bHLH), and WD40 repeat proteins were discovered based on transcriptome dataset. Therefore, this study presents the first survey of transcriptome on the flower of S. chamaejasme to discover the major candidate genes involved in flavonoid biosynthesis pathway. These results will promote an understanding of the genetic mechanism of flavonoid biosynthesis in S. chamaejasme. At the same time, this transcriptome dataset can serve as an important public information platform for gene expression, genomic and functional genomic studies in this species.