Candidate genes of flavonoid biosynthesis in Selaginella bryopteris (L.) Baker identified by RNA-Seq

In the present study, de novo transcriptome analysis of Selaginella bryopteris in frond and root was performed to understand the regulation of flavonoid (FL) biosynthesis. High-quality data of 5.84 and 5.86 Gb was generated for frond and root, respectively, that assembled into 94,713 and 81,567 transcripts. A total of 87,471 and 73,395 unigenes were obtained from frond and root, respectively. A total of 41,267 and 31,048 CDS of frond and root, respectively, were annotated by BLASTX, which showed maximum hits against S. moellendorffii. Out of 11,285 differentially expressed genes, a total of 5639 genes were found to be down-regulated and 5628 genes up-regulated in frond as compared to those in root. In silico analysis of expression of genes in frond as compared to that in root was done for those related to phenylpropanoid (PP)/FL biosynthesis along with transcription factors (TFs) after DESeq and MapMan-based information. Results showed that genes of PP/FL biosynthesis pathway namely SbCHS, SbCHI, SbF3H, SbF3'H, SbDFR, SbUF3GT, SbCCOAMT, and SbCATOMT and TFs (SbMYB1, SbMYB2, SbMYB3, SbBHLH1, and SbWD40-5) were up-regulated in frond in comparison to those in root. Further, this in silico expression data was validated by RT-PCR analysis which showed predominant expression of most of these genes in frond and indicated their importance in the biosynthesis of flavonoids in S. bryopteris. A total of 9074 simple sequence repeats (SSRs) were also identified for frond and 3811 SSRs for root; these can be used for experimental validation.