Comparative transcriptome profiling and co-expression network analysis reveals functionally coordinated genes associated with metabolic processes of Andrographis paniculata

Abstract

Natural products and secondary metabolites are produced through plant biosynthetic pathways and hold enormous opportunities for treating human ailments. Andrographis paniculata (Kalmegh), commonly known as “king of bitters” is widely exploited for its usage in array of polyherbal formulations. Andrographolide, a diterpene lactone is the major bioactive metabolite with widespread pharmaceutical properties, extracted primarily from the leaves of this plant. Using high throughput NGS (next generation sequencing), we have generated whole transcriptome profile of leaves of A. paniculata using semiconductor-based Ion Torrent technology. Functional annotation of transcripts revealed 20,498 unigenes annotating to plant nr database with 8695 belonging to biological processes, 7605 to molecular function and 14,448 to cellular component. KEGG pathway analysis annotated 2592 transcripts to different biological pathways with 631 mapping to metabolic pathways, 297 to secondary metabolic pathways and 157 to biosynthesis of antibiotics etc. Additionally, to enrich the information, a co-expression analysis was performed with publically available datasets generating an expression matrix of 4270 genes. Co-expression analysis using WGCNA package revealed 10 transcripts as major hub/bottleneck genes known to be majorly involved in developmental and metabolic processes of plants e.g. flower development (POE52202.1, protein heading date 3a), oxidoreductase activity and lipid metabolic process (PIN06124.1, Delta (12)-fatty acid dehydrogenase) etc., implying the impact of genetic as well as environmental factors on their expression.