Comparative transcriptome analysis to identify candidate genes related to chlorogenic acid biosynthesis in Eucommia ulmoides Oliv.

Abstract

We performed a comparative transcriptome between two different concentrations of CGA from leaves in E. ulmoides. The key genes in the biosynthesis of CGA were identified by differential expression analysis. Eucommia ulmoides Oliv. is native to China and famous for its extensive medicinal value, such as anti-fatigue, anti-aging, and enhanced immunity, etc. Chlorogenic acid (CGA) is the main medicinal ingredient of E. ulmoides. In E. ulmoides, the gene functions related to CGA biosynthesis are not fully understood. In this study, we conducted Illumina transcriptome sequencing and digital gene expression (DGE) for E. ulmoides with high content of CGA (H01, H02, and H03) and low content of CGA (L01, L02, and L03) to explore the potential genes involved in CGA biosynthesis. A total of 82,065 unigenes were generated. Of these unigenes, 28 were involved in CGA biosynthesis pathways and 116 regulated the CGA biosynthesis. Furthermore, by gene expression profiling and differential expression analysis, three functional genes including two PALs (c133625.graph_c5 and c133625.graph_c7), one 4CL (c139078.graph_c0), and three transcription factors (TFs), including one ERF2 (c139016.graph_c3) and two WRKY (c139022.graph_c3 and c139022.graph_c0) were different expressed, these genes may play key roles in CGA biosynthesis. This study will provide useful genomic resources for the investigation of CGA biosynthesis and genetic improvements of E. ulmoides.