Re-analysis of RNA-Sequencing Data on Apple Stem Grooving Virus infected Apple reveals more significant differentially expressed genes

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  1. Bipin Balan1,2,
  2. Lijin K. Gopi3,
  3. Dhinoth Kumar Bangaruswamy3

Authors Affiliation(s)

  • 1SciGenom Research Foundation, Kamala Govind Estate, Cheruthuruthy, Kerala, INDIA
  • 2Dipartimento di Scienze Agrarie Alimentari e Forestali, Università 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

Abstract

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 [1] 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.

References

  1. Chen, S., Ye, T., Hao, L., Chen, H., Wang, S., Fan, Z., et al. (2014) Infection of apple by apple stem grooving virus leads to extensive alterations in gene expression patterns but no disease symptoms. PLoS ONE 9: e95239-e95239. Crossref