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Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome

Sunflowers (Helianthus annuus L.) are susceptible to multiple diseases in field production. In this study, we collected diseased sunflower leaves in fields located in South Dakota, USA, for virome investigation. The leaves showed visible symptoms on the foliage, indicating phomopsis and rust infecti...

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Autores principales: Wang, Ziyi, Neupane, Achal, Feng, Jiuhuan, Pedersen, Connor, Lee Marzano, Shin-Yi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473204/
https://www.ncbi.nlm.nih.gov/pubmed/34578448
http://dx.doi.org/10.3390/v13091867
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author Wang, Ziyi
Neupane, Achal
Feng, Jiuhuan
Pedersen, Connor
Lee Marzano, Shin-Yi
author_facet Wang, Ziyi
Neupane, Achal
Feng, Jiuhuan
Pedersen, Connor
Lee Marzano, Shin-Yi
author_sort Wang, Ziyi
collection PubMed
description Sunflowers (Helianthus annuus L.) are susceptible to multiple diseases in field production. In this study, we collected diseased sunflower leaves in fields located in South Dakota, USA, for virome investigation. The leaves showed visible symptoms on the foliage, indicating phomopsis and rust infections. To identify the viruses potentially associated with the disease diagnosed, symptomatic leaves were obtained from diseased plants. Total RNA was extracted corresponding to each disease diagnosed to generate libraries for paired-end high throughput sequencing. Short sequencing reads were assembled de novo and the contigs with similarities to viruses were identified by aligning against a custom protein database. We report the discovery of two novel mitoviruses, four novel partitiviruses, one novel victorivirus, and nine novel totiviruses based on similarities to RNA-dependent RNA polymerases and capsid proteins. Contigs similar to bean yellow mosaic virus and Sclerotinia sclerotiorum hypovirulence-associated DNA virus were also detected. To the best of our knowledge, this is the first report of direct metatranscriptomics discovery of viruses associated with fungal infections of sunflowers bypassing culturing. These newly discovered viruses represent a natural genetic resource from which we can further develop potential biopesticide to control sunflower diseases.
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spelling pubmed-84732042021-09-28 Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome Wang, Ziyi Neupane, Achal Feng, Jiuhuan Pedersen, Connor Lee Marzano, Shin-Yi Viruses Article Sunflowers (Helianthus annuus L.) are susceptible to multiple diseases in field production. In this study, we collected diseased sunflower leaves in fields located in South Dakota, USA, for virome investigation. The leaves showed visible symptoms on the foliage, indicating phomopsis and rust infections. To identify the viruses potentially associated with the disease diagnosed, symptomatic leaves were obtained from diseased plants. Total RNA was extracted corresponding to each disease diagnosed to generate libraries for paired-end high throughput sequencing. Short sequencing reads were assembled de novo and the contigs with similarities to viruses were identified by aligning against a custom protein database. We report the discovery of two novel mitoviruses, four novel partitiviruses, one novel victorivirus, and nine novel totiviruses based on similarities to RNA-dependent RNA polymerases and capsid proteins. Contigs similar to bean yellow mosaic virus and Sclerotinia sclerotiorum hypovirulence-associated DNA virus were also detected. To the best of our knowledge, this is the first report of direct metatranscriptomics discovery of viruses associated with fungal infections of sunflowers bypassing culturing. These newly discovered viruses represent a natural genetic resource from which we can further develop potential biopesticide to control sunflower diseases. MDPI 2021-09-18 /pmc/articles/PMC8473204/ /pubmed/34578448 http://dx.doi.org/10.3390/v13091867 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
Wang, Ziyi
Neupane, Achal
Feng, Jiuhuan
Pedersen, Connor
Lee Marzano, Shin-Yi
Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome
title Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome
title_full Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome
title_fullStr Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome
title_full_unstemmed Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome
title_short Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome
title_sort direct metatranscriptomic survey of the sunflower microbiome and virome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473204/
https://www.ncbi.nlm.nih.gov/pubmed/34578448
http://dx.doi.org/10.3390/v13091867
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