Regulation of specialized metabolites by long non-coding RNAs in Camellia sinensis

Abstract The tea plant (Camellia sinensis) possesses an array of specialized metabolites that contribute to its distinctive flavor and health-promoting properties. How they are regulated by long non-coding RNAs (lncRNAs) is not well elucidated. Here we systematically identify 65 675 high-confidence lncRNAs using the RNA sequencing dataset from the second-leaf samples of 133 accessions. Integrative co-expression analysis revealed 55 lncRNA-centered regulatory modules significantly associated with the accumulation of 57 specialized metabolites. We further show that a Gypsy-retrotransposon-derived lncRNA, CsLNC703, promotes CsMYB111-mediated regulation of the F3′H-associated flavan-3-ol biosynthetic branch, resulting in preferential accumulation of catechin (C), epicatechin (EC), and epicatechin gallate (ECG). These findings demonstrate that lncRNAs constitute an important regulatory layer controlling specialized metabolism in tea plants and reveal a transposon-derived lncRNA that modulates catechin biosynthesis. Our study provides new insights into the regulatory mechanisms underlying metabolic diversity in tea and highlights lncRNAs as potential targets for metabolic engineering and breeding of tea cultivars with improved quality traits.