Identification and analysis of the bZIP gene family in Rheum palmatum based on full-length transcriptome sequencing

bZIP transcription factors play crucial roles in the regulation of plant growth and development, biosynthesis of secondary metabolites, and responses to various stresses. In this study, the bZIP gene family was systematically identified from Rheum palmatum using full-length transcriptome sequencing data. Bioinformatic tools were used to analyze the physicochemical properties, motif compositions, and evolutionary relationships of the bZIPs. RNA-seq was used for tissue expression analysis and to evaluate responses to MeJA (methyl jasmonate) treatment. Overall, we found that R. palmatum had 63 bZIP gene family members, namely RpbZIP1～RpbZIP63, which could be divided into 11 subfamilies, i.e., A～I, K and S, according to their phylogenetic relationship with Arabidopsis. The RpbZIPs gene mainly encodes unstable hydrophilic proteins, all of which were predicted to localize in the nucleus. The protein secondary structure was mainly α helix and random curling. RNA-Seq revealed that six genes, including RbZIP16, RpbZIP17, and RpbZIP61, etc. were highly expressed in the roots and rhizomes of R. palmatum, as well as being responsive to MeJA treatment. qPCR verified that four of them were consistent with the expression level of RNA-Seq results. This study systematically analyzed the bZIP gene family of R. palmatum, providing a scientific basis for further studies on gene function and the transcriptional regulation mechanisms of secondary metabolism of rhubarb.