De novo assembly, annotation and molecular marker identification from the leaf transcriptome of Ocimum gratissimum L

Abstract

Abstract Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.