Integrating GC-MS and ssRNA-Seq analysis to identify long non-coding RNAs related to terpenoid biosynthesis in Cinnamomum camphora

Abstract

Terpenoids are the main constituents in the leaf essential oil (LEO) of Cinnamomum camphora, which has long been considered an important raw material for food, cosmetic and pharmaceutical industries. However, most previous studies have concentrated more on the functions of structural genes and microRNAs in terpenoid biosynthesis pathways. Long non-coding RNAs (lncRNAs) related to terpenoid biosynthesis are rarely reported. Here, the components of LEOs in cineole-, linalool- and nerolidol-type C. camphora were determined by gas chromatography-mass spectrometry (GC–MS). Strand-specific RNA sequencing (ssRNA-seq) was used to identify lncRNAs involved in terpenoid biosynthesis in three chemotypes of C. camphora. A total of 8826 lncRNAs were first classified in C. camphora: 4331 long intergenic noncoding RNAs (lincRNAs), 1410 antisense lncRNAs, and 3085 sense overlapping lncRNAs. Among these lncRNAs, 243, 343, and 252 were classified as cineole-, linalool- and nerolidol-specific lncRNAs, respectively. Many target genes of differentially expressed lncRNAs (DELs) were enriched in terpenoid biosynthesis pathways, and 17 DELs were related to monoterpenoid and sesquiterpenoid biosynthesis. Moreover, we also constructed lncRNA–protein-coding gene (PCgenes) regulatory networks for terpenoid biosynthesis. This study supplies precious genetic resources to further research on lncRNA functions and their role in the regulatory mechanism of terpenoid biosynthesis.