Distribution survey, phytochemical and transcriptome analysis to identify candidate genes involved in biosynthesis of functional components in Zanthoxylum nitidum.

• Thirty-five wild Z. nitudum samples from different growing sites were collected and attributed to four types. • Five active compounds including three alkaloids, one linnan, and one flavonoid were characterized by Ultra Performance Liquid Chromatography. • The nine transcriptome libraries of type III and three libraries of type I were performed. • 77 candidate unigenes involved in biosynthesis pathway of five active compounds were identified. • Providing us insight into resource preservation and the potential of molecular breeding for improving the quality of Z. nitidum. The dried roots of Zanthoxylum nitidum (Roxb.) DC have been widely used in Chinese medicine for the treatment of rheumatoid arthritis, toothache, stomach ache, bruises, and snakebites. Alkaloid content, particularly for nitidine chloride (NC), is a crucial indicator of herb quality. Abuse of plant sources of Z. nitidum , such as the usage of NC content not adhering to the Chinese Pharmacopoeia specification, has appeared in herb markets. Thus, a distribution survey was conducted on wild samples from 35 sites grown in 5 provinces, including the evaluation of morphological and phytochemical differences (three alkaloids, one flavonoid, and one lignin). Consequently, the surveyed plants were attributed to four types: three species (type I, II, and III) and one variety (type IV). The NC content of most type I, II, and III plants met quality guidelines, however, all three type IV plants from Guangxi Province exhibited low NC content; the use of plants from that area should be carefully considered. To identify the biosynthetic pathway of NC and other active compounds, nine transcriptomes of type III (root, stem and leaf, three replicates for each tissue) and three of type I (three leaf replicates) were performed to mine candidate unigenes. A set of 505,386 unigenes with an average length of 866 bp were identified. Coexpression analysis of tissue expression patterns were used to narrow down the candidate genes. Consequently, 23 candidate unigenes involved in the alkaloid biosynthesis pathway, 38 unigenes in the lignan biosynthesis pathway, and 16unigenes in the flavonoid biosynthesis pathway were screened. The distribution survey and phytochemical and transcriptome analyses conducted in this study provided valuable insights into resource preservation and the potential of molecular breeding to improve the quality of Z. nitidum products. [ABSTRACT FROM AUTHOR]