Transcriptomic analysis reveals candidate genes for phenolic acid biosynthesis in Polygonum chinense L.

Polygonum chinense L. (synonym: Persicaria chinensis) was considered a medicinal food homology plant, which was often used in herbal tea. This plant is rich in phenolic acid compounds that possess antibacterial, antioxidant, and other pharmacological properties. Although phenolic acids of P. chinense have been investigated pharmacologically, the genetic basis of phenolic acid biosynthesis in this plant is unknown due to the lack of a reference genome. In this study, we employed a combination of transcriptomics and bioinformatic analysis to construct a transcriptome database for three tissues (flowers, leaves, and stems) of P. chinense, and extracted genes related to the biosynthesis of phenolic acids. In total, 90,635 unigenes with a mean length of 1,224 bp were obtained, 70,915 of which were functionally annotated. Seventy-eight differentially expressed genes (DEGs) associated with the phenolic acid biosynthetic pathway were identified, with five DEGs (CL4812-1, CL7291-1, CL5600-1, CL6332-3, and Unigene12384) being singled out as candidate genes putatively involved in the regulation of phenolic acid biosynthesis through correlation analysis. A comprehensive sequence analysis of these candidate genes was subsequently performed. The phylogenetic tree and the structural model were constructed, and molecular docking studies were conducted for the 4-coumarate-CoA ligase. Additionally, the expression levels of 12 unigenes encoding key enzymes involved in phenolic acid biosynthesis were validated using quantitative reverse transcription-PCR. Our study provides candidate genes at the transcriptional level for further investigation of the molecular regulatory mechanisms involved in phenolic acid biosynthesis, as well as a scientific basis for the development of P. chinense as a food-medicine dual-purpose plant.