Transcriptome and metabolome jointly analyze the raspberry prickle formation mechanism of raspberry prickles

The prickles are widespread in plants and play an important role in defense mechanisms and ecological adaptation. As a plant with high economic value, the development and formation of prickles in raspberries pose challenges to fruit harvesting and production management, which greatly limits the development of the raspberry industry. To investigate the developmental mechanism of raspberry prickles, we sequenced and analyzed the transcriptome and metabolome of primary, secondary, and tertiary lateral branches of different raspberries. The results showed that lignin biosynthesis genes, cellulose biosynthesis genes, etc. were highly expressed during prickle formation, phenylpropanoid biosynthesis, cuticle, cork, and wax biosynthesis, and phytohormone signaling were the key pathways for prickles to complete the development of lignification during prickle development. PAL2, ACAT2, 4CL3, CCR1, CHS2, FLS, GA2, WRKY, bHLH, and MYB genes were differentially expressed during the development of different contrasting groups of raspberry prickles. From this, we hypothesized that these genes may be associated with the developmental mechanisms of raspberry prickles and may be key genes involved in the development of raspberry prickles with tissue-specific expression. This study lays the foundation for further analysis of the molecular mechanism of plant prickle development.