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HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection

Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive...

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Autores principales: Malapi-Wight, Martha, Adhikari, Bishwo, Zhou, Jing, Hendrickson, Leticia, Maroon-Lango, Clarissa J., McFarland, Clint, Foster, Joseph A., Hurtado-Gonzales, Oscar P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402784/
https://www.ncbi.nlm.nih.gov/pubmed/34452491
http://dx.doi.org/10.3390/v13081627
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author Malapi-Wight, Martha
Adhikari, Bishwo
Zhou, Jing
Hendrickson, Leticia
Maroon-Lango, Clarissa J.
McFarland, Clint
Foster, Joseph A.
Hurtado-Gonzales, Oscar P.
author_facet Malapi-Wight, Martha
Adhikari, Bishwo
Zhou, Jing
Hendrickson, Leticia
Maroon-Lango, Clarissa J.
McFarland, Clint
Foster, Joseph A.
Hurtado-Gonzales, Oscar P.
author_sort Malapi-Wight, Martha
collection PubMed
description Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.
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spelling pubmed-84027842021-08-29 HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection Malapi-Wight, Martha Adhikari, Bishwo Zhou, Jing Hendrickson, Leticia Maroon-Lango, Clarissa J. McFarland, Clint Foster, Joseph A. Hurtado-Gonzales, Oscar P. Viruses Article Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses. MDPI 2021-08-17 /pmc/articles/PMC8402784/ /pubmed/34452491 http://dx.doi.org/10.3390/v13081627 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Malapi-Wight, Martha
Adhikari, Bishwo
Zhou, Jing
Hendrickson, Leticia
Maroon-Lango, Clarissa J.
McFarland, Clint
Foster, Joseph A.
Hurtado-Gonzales, Oscar P.
HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection
title HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection
title_full HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection
title_fullStr HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection
title_full_unstemmed HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection
title_short HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection
title_sort hts-based diagnostics of sugarcane viruses: seasonal variation and its implications for accurate detection
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402784/
https://www.ncbi.nlm.nih.gov/pubmed/34452491
http://dx.doi.org/10.3390/v13081627
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