Virome in commercial wine grapes: identification of viruses and their genetic variants using RNA-Sequencing data

Advisor:
Baozhong Meng (MCB)

As a perennial plant crop, grapevine is known to be infected with multiple viruses and viroids at the same time. Viral infections are difficult to identify by sole examination of host symptoms. Conventional molecular virus detection methods such as Polymerase chain reaction (PCR) are virus-specific, thereby lacking the ability in the identification of novel viruses and viral strains. RNA-Sequencing (RNA-Seq) of virus-infected grapevine produce massive amounts of information of genome sequence of the infecting viruses; therefore, RNA-Seq allows screening of both known and novel viral sequences in a given sample. Challenges in using high-throughput sequencing (HTS) for virus screening involves its non-standardized pipelines and multiple steps of bioinformatics analysis with various choices of tools.

The proposed research involves the analysis of sequence data obtained from RNA-Seq of virus-infected commercial grapevine obtained in our laboratory and the identification of viruses. The goal of this project is to develop a bioinformatics pipeline that can accurately and efficiently identify existing viral genomes of the RNA-Seq. Upon successful development of pipeline, the student may also conduct comparison between developed pipeline and Virtool - a web-based application of plant virus detection developed by Canadian Food Inspection Agency (CFIA).

This project will include the following objectives:

  1. Use appropriate bioinformatics tools to process raw sequence data generated from RNA-Seq, including trimming, quality check, and sequence alignment.
  2. Develop an effective pipeline to filter host (grapevine) genome, locate genomes of viruses from the filtered RNA-Seq, and identification of variants of the obtained genomes of viruses.
  3. Comparison of identified viruses and viral strains by developed pipeline by the student and Virtool.