Your browser doesn't support javascript.
loading
Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants.
Lelwala, Ruvini V; LeBlanc, Zacharie; Gauthier, Marie-Emilie A; Elliott, Candace E; Constable, Fiona E; Murphy, Greg; Tyle, Callum; Dinsdale, Adrian; Whattam, Mark; Pattemore, Julie; Barrero, Roberto A.
Afiliação
  • Lelwala RV; eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia.
  • LeBlanc Z; Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia.
  • Gauthier MA; eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia.
  • Elliott CE; eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia.
  • Constable FE; Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia.
  • Murphy G; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia.
  • Tyle C; Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia.
  • Dinsdale A; Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia.
  • Whattam M; Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia.
  • Pattemore J; Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia.
  • Barrero RA; Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia.
Viruses ; 14(7)2022 07 05.
Article em En | MEDLINE | ID: mdl-35891459
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.
Assuntos
Palavras-chave

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Vírus de Plantas / Viroides / Pequeno RNA não Traduzido Idioma: En Ano de publicação: 2022 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Vírus de Plantas / Viroides / Pequeno RNA não Traduzido Idioma: En Ano de publicação: 2022 Tipo de documento: Article