Identification and characterization of protein coding genes in monsonia (Monsonia burkeana Planch. ex harv) using a combination of approaches

Abstract

The advent of next generation sequencing has made possible massive availability of sequence information for in-depth structural and functional analysis of the genes and their encoded biological state in model and non-model organisms. In this study, we demonstrate a combinatorial approach for finding protein coding genes using ab initio and extrinsic evidence-based methods in monsonia (Monsonia burkeana Planch. ex harv). This is an important herbal tea crop, yet little is known about its coding genes. To our knowledge, this is the first description of protein coding genes with detailed functional annotation in M. burkeana. This study demonstrates that (1) regions of transcript assembly potentially encode protein coding genes, (2) homologous evidence with known functions reliably assigns functions to the identified genes (3) conserved domains suggest evolutionary and functional relationship of the crop with other lineage and (4) accuracy of finding coding genes in alignment free models and in RNA-seq alignment based transcript assembly performs well. This study provides a glimpse of functional information of the protein coding region at the transcriptome level and can be used as the basis for further investigation of the underlying genetic composition and molecular functions associated with M. burkeana.