Lakshmi Priya, P. M. and K. K. Sabu.
In Silico Analysis of Transcriptomes of Catharanthus roseus and Rauvolfia serpentina, two potent medicinal plants using a pipeline developed from publicly available tools.
American Journal of Bioinformatics Research 5(2): 21-25 (2015)
doi:10.5923/j.bioinformatics.20150502.01
Until recently, there was no data available on the genome sequences of medicinal plants. But now, public databases for the transcriptomes of important medicinal plants are available. But an analysis pipeline effectively combining publicly available tools is lacking which would otherwise enable in-depth analysis of the transcriptomes. In this context, we have developed an effective in silico analysis pipeline using tools such as FastQC, FastQ Groomer, TopHat, Cufflinks, Cuffmerge and Cuffdiff available in Galaxy platform and other tools such as DAVID, ExPASy, MetaCyc and PlantCyc. We have tested the pipeline for comparative analysis of the transcriptome of Catharanthus roseus (L.) G.Don and Rauvolfia serpentina (L.) Benth. ex Kurz, two well-known medicinal plants. This study identified genes that are similarly expressing in the roots of these plants leading to the formation of the same secondary metabolite, “Strictosidine” and also identified differentially expressing genes in the leaves of C. roseusand R. serpentina lead to the formation of different metabolites, “Vinblastine” and “Ajmaline”. The findings of the study indicated that the pipeline developed is effective and helped to analyze the transcriptomes and expression data.
