Comparative transcriptome analysis identifies putative genes involved in secondary metabolite biosynthesis in Euphorbia maculata

Euphorbia maculata L. is an annual plant, belonging to Euphorbiaceae family that can produce anti-inflammatory and biologically important compounds like terpenoids, tannins and polyphenols. Despite the importance of E maculata, there is very limited genetic information. In this study, we conducted full-length cDNA characterization using the SMRT sequencing of PacBio to investigate comprehensive reference gene information and isoform copy number in metabolite biosynthesis. In addition, we sequenced E. maculata transcriptomes obtained from leaves, roots and stems using Illumina short read to identify differential expressed genes in the metabolite biosynthesis pathways. PacBio generated 62 million polymerase read out of which 81,433 high quality reads were obtained that were further processed to reconstruct a genome of 20,722 reads. Of the total genes, 44% were having at least two or more isoforms. More than 92% of unigenes were successfully annotated in various databases like Nr, Pfam, GO and KEGG. Plant transcription factors (TF) database annotated 1,564 putative E. maculata unigenes in 46 TF families, of which, ARF and MYB-related were among the highest annotated. Multiple candidate genes encoding for enzymes in tocopherol biosynthesis, polyphenol and flavonol biosynthetic pathways were identified. Our transcriptome data and related findings would provide valuable genetic resources for studying various biochemical processes of E maculata, particularly the biosynthesis of terpenoids