Whole transcriptome sequencing from Zanthoxylum armatum: implications on metabolic pathway analysis and regulation

Zanthoxylum armatum, a deciduous aromatic shrub has been utilized by traditional healers for treatment of various ailments. Elucidation of the transcriptome data and expression studies of the putative biosynthetic pathway gene(s) of berberine and sanguinarine production in leaf, stem, and fruit at different seasons and identification of transcription factor families involved in the biosynthesis of isoquinoline alkaloids was established in the present study. The assembled transcripts were clustered into 44254, 46402 and 46521 unigenes and a total of 32118, 27777 and 19754 CDS were predicted from unigenes in fruit, leaf and stem samples respectively. Using MISA 5576 SSRs were identified from fruit, leaf and stem samples, out of which a total of 1877 SSRs with 150 flanking regions were predicted. Putative biosynthetic pathway genes like BBE, BBE-like, SOMT, CAS, STOX, BS and SR were significantly expressed in the three samples of the plant in different seasons and at different level. Transcription factor analysis along with correlation matrix predicted abundant families like AP2/ERF family (4010), followed by MYB-related family (3010), RPL2 family (2760), MYC family (2662), DREB/CRF family (2526), and RAV (2302) to be the regulators along with WRKY. The association analysis of the metabolome and the assembled transcriptome from Zanthoxylum armatum will go a long way in re-engineering of the species by AI assisted priming. The TFs would enable artificial intelligence-based designing of efficient minipromoters for enhancing the production of the target compounds in a more efficient and predictable manner.