Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants Article Swipe
Ruvini Lelwala
,
Zacharie LeBlanc
,
Marie Gauthier
,
Candace E. Elliott
,
Fiona Constable
,
Greg Murphy
,
Callum Tyle
,
Adrian Dinsdale
,
Mark Whattam
,
Julie Pattemore
,
Roberto A. Barrero
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/v14071480
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/v14071480
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.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/v14071480
- https://www.mdpi.com/1999-4915/14/7/1480/pdf?version=1657173330
- OA Status
- gold
- Cited By
- 7
- References
- 66
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4284688876
All OpenAlex metadata
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https://openalex.org/W4284688876Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3390/v14071480Digital Object Identifier
- Title
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Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in PlantsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-07-05Full publication date if available
- Authors
-
Ruvini Lelwala, Zacharie LeBlanc, Marie Gauthier, Candace E. Elliott, Fiona Constable, Greg Murphy, Callum Tyle, Adrian Dinsdale, Mark Whattam, Julie Pattemore, Roberto A. BarreroList of authors in order
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https://doi.org/10.3390/v14071480Publisher landing page
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https://www.mdpi.com/1999-4915/14/7/1480/pdf?version=1657173330Direct link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.mdpi.com/1999-4915/14/7/1480/pdf?version=1657173330Direct OA link when available
- Concepts
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Quarantine, Virology, Virus, Biology, Web application, Computer science, Bioinformatics, Computational biology, World Wide Web, EcologyTop concepts (fields/topics) attached by OpenAlex
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7Total citation count in OpenAlex
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2025: 2, 2024: 2, 2023: 3Per-year citation counts (last 5 years)
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66Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.fraction | 169 |
| abstract_inverted_index.imported | 141, 157, 199 |
| abstract_inverted_index.indexing | 99 |
| abstract_inverted_index.validate | 117 |
| abstract_inverted_index.viruses. | 107 |
| abstract_inverted_index.workflow | 192 |
| abstract_inverted_index.(PVirDB). | 91 |
| abstract_inverted_index.Australia | 66 |
| abstract_inverted_index.algorithm | 173 |
| abstract_inverted_index.conducted | 135 |
| abstract_inverted_index.detecting | 72 |
| abstract_inverted_index.diagnosis | 138 |
| abstract_inverted_index.expertise | 40 |
| abstract_inverted_index.megablast | 172 |
| abstract_inverted_index.pathogens | 154 |
| abstract_inverted_index.processed | 143 |
| abstract_inverted_index.resources | 38 |
| abstract_inverted_index.screening | 29, 197 |
| abstract_inverted_index.web-based | 61 |
| abstract_inverted_index.workflows | 63 |
| abstract_inverted_index.Australia. | 150 |
| abstract_inverted_index.Sequencing | 108 |
| abstract_inverted_index.databases. | 53 |
| abstract_inverted_index.detection. | 18 |
| abstract_inverted_index.developed: | 55 |
| abstract_inverted_index.discovered | 160 |
| abstract_inverted_index.post-entry | 146 |
| abstract_inverted_index.quarantine | 33, 147 |
| abstract_inverted_index.resources. | 119 |
| abstract_inverted_index.sequencing | 1, 95 |
| abstract_inverted_index.bottlenecks | 21 |
| abstract_inverted_index.implemented | 93 |
| abstract_inverted_index.large-scale | 137, 184 |
| abstract_inverted_index.sensitivity | 176 |
| abstract_inverted_index.successful, | 183 |
| abstract_inverted_index.GA-VirReport | 68, 113 |
| abstract_inverted_index.availability | 46 |
| abstract_inverted_index.command-line | 42 |
| abstract_inverted_index.cross-sample | 131 |
| abstract_inverted_index.environments | 43 |
| abstract_inverted_index.implementing | 23 |
| abstract_inverted_index.specificity. | 178 |
| abstract_inverted_index.computational | 37 |
| abstract_inverted_index.user-friendly | 190 |
| abstract_inverted_index.bioinformatics | 62, 191 |
| abstract_inverted_index.contamination. | 132 |
| abstract_inverted_index.implementation | 185 |
| abstract_inverted_index.High-throughput | 0 |
| abstract_inverted_index.GA-VirReport-Stats | 70 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5042291484 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 11 |
| corresponding_institution_ids | https://openalex.org/I160993911 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/9 |
| sustainable_development_goals[0].score | 0.47999998927116394 |
| sustainable_development_goals[0].display_name | Industry, innovation and infrastructure |
| citation_normalized_percentile.value | 0.84008428 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |