Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants

Ruvini V Lelwala; Zacharie LeBlanc; Marie-Emilie A Gauthier; Candace E Elliott; Fiona E Constable; Greg Murphy; Callum Tyle; Adrian Dinsdale; Mark Whattam; Julie Pattemore; Roberto A Barrero

doi:10.3390/v14071480

Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants

Viruses. 2022 Jul 5;14(7):1480. doi: 10.3390/v14071480.

Authors

Affiliations

¹ eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia.
² Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia.
³ Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia.
⁴ Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia.
⁵ Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia.

Abstract

High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21-22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ.

Keywords: VirReport; high-throughput sequencing; plant virus and viroid detection; post-entry quarantine; small RNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Internet
Pilot Projects
Plant Diseases
Plant Viruses* / genetics
Plants
Quarantine
RNA, Plant
RNA, Small Untranslated*
Viroids* / genetics

Substances

RNA, Plant
RNA, Small Untranslated

Grants and funding

This research was funded by the Biosecurity Innovation Program, project number 202048, and in part by the Hort Innovation, project number MT18005, ‘Improving plant industry access to new genetics through faster and more accurate diagnostics using Next Generation Sequencing (NGS)’ using the Hort Innovation Citrus, Grape Tables, Rubus, Potato and Nursery research and development levy, co-investment from Queensland University of Technology and contributions from the Australian Government. Hort Innovation is the grower-owned, not-for-profit research and development corporation for Australian horticulture.