De novo transcriptome analysis of Argemone mexicana plant (SRR287649) and annotation for secondary metabolite producing genes

Abstract

Argemone mexicana (family: Papaveraceae) is an important medicinal plant that produces a wide range of secondary metabolites. In this study, the RNA-seq data of Argemone mexicana plant stem was retrieved from the NCBI SRA database (SRR287649). The quality checking and trimming of the raw data were performed by using FastQC, Cutadapt and Trimmomatic 0.39 software. Further, de-novo sequence assembly by Trinity software package generated a total 29591 number of contig sequences. As subsequent work, BLASTX and annotation of all the contig by using Blast2GO and WEGO2 tool produced 19780 annotated genes with 44440 gene ontology (GO) terms. Further, the genes involved in secondary metabolite production of the Argemone mexicana plant were predicted by functional assignment of the contig sequences.