- 1SciGenom Research Foundation, Kamala Govind Estate, Cheruthuruthy, Kerala, INDIA
- 2Dipartimento di Scienze Agrarie Alimentari e Forestali, UniversitÃ degli Studi di Palermo, Palermo, ITALY
- 3AgriGenome Labs Private Limited, Smart City Kochi, Infopark Road, Kakkanad, Kerala, INDIA
Can J Biotech, Volume 1, Special Issue-Supplement, Page 294, DOI: https://doi.org/10.24870/cjb.2017-a278
RNA sequencing (RNA-Seq) technology has enabled the researchers to investigate the host global gene expression changes in plant-virus interactions which helped to understand the molecular basis of virus diseases. The re-analysis of RNA-Seq studies using most updated genome version and the available best analysis pipeline will produce most accurate results. In this study, we re-analysed the Apple stem grooving virus (ASGV) infected apple shoots in comparison with that of virus-free in vitro shoots  using the most updated Malus x domestica genome downloaded from Phytozome database. The re-analysis was done by using HISAT2 software and Cufflinks program was used to mine the differentially expressed genes. We found that ~20% more reads was mapped to the latest genome using the updated pipeline, which proved the significance of such re-analysis. The comparison of the updated results with that of previous was done. In addition, we performed protein-protein interaction (PPI) to investigate the proteins affected by ASGV infection.
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