Sneha Murmu

Lathyrus has a great agronomic importance as it is grown for both human consumption and livestock feed and is well adapted to the arid conditions and is one of the hardiest pulses known till date. Together with the growing popularity of RNA Seq, a number of data analysis methods and pipelines have already been developed for transcriptome analysis. There is a common assumption that substantial gains occur in the quality of the results as read length increases and when paired-ends (PE) are used. Currently, however, there are no clear consensus about the best practices for SOLiD short read single end data, which makes the choice of an appropriate method a daunting task especially for a basic user. Hence a comparative study of RNA-Seq analysis tools, in this study commercialized CLC bio Genomics Workbench vs open-source software like Velvet-Oases and TopHat-Cufflinks for de novo and reference-genome based approach respectively, was made with the aim to understand and assist the choice of selection of such methods for SOLiD transcriptome data. Velvet-Oases and TopHat-Cufflinks were chosen to carry out the transcriptome analysis of Lathyrus sativus based on their performance against Glycine max test dataset. Drought negatively impacts plant growth and the productivity of crops around the world. Understanding the molecular mechanisms in the drought response is important for improvement of drought tolerance using molecular techniques. In this study, we found 57 differentially expressed genes in case of de novo based approach and 140 in case of reference-genome based approach. The findings of this study is expected to facilitate the decision of choosing an optimal tools for the analysis of short read SOLiD transcriptome data. The result is also expected to provide an improved understanding and identification of sources for resistance against moisture stress for future genetic research in this hitherto under-researched, valuable legume crop.