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Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana

Virus infestation can seriously harm the host plant’s growth and development. Turnip yellows virus (TuYV) infestation of host plants can cause symptoms, such as yellowing and curling of leaves and root chlorosis. However, the regulatory mechanisms by which TuYV affects host growth and development ar...

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Autores principales: Yu, Ruiyang, Ye, Xinghuo, Zhang, Chenghua, Hu, Hailong, Kang, Yanlei, Li, Zhong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9858106/
https://www.ncbi.nlm.nih.gov/pubmed/36661502
http://dx.doi.org/10.3390/cimb45010016
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author Yu, Ruiyang
Ye, Xinghuo
Zhang, Chenghua
Hu, Hailong
Kang, Yanlei
Li, Zhong
author_facet Yu, Ruiyang
Ye, Xinghuo
Zhang, Chenghua
Hu, Hailong
Kang, Yanlei
Li, Zhong
author_sort Yu, Ruiyang
collection PubMed
description Virus infestation can seriously harm the host plant’s growth and development. Turnip yellows virus (TuYV) infestation of host plants can cause symptoms, such as yellowing and curling of leaves and root chlorosis. However, the regulatory mechanisms by which TuYV affects host growth and development are unclear. Hence, it is essential to mine small RNA (sRNA) and explore the regulation of sRNAs on plant hosts for disease control. In this study, we analyzed high-throughput data before and after TuYV infestation in Arabidopsis using combined genetics, statistics, and machine learning to identify 108 specifically expressed and critical functional sRNAs after TuYV infection. First, comparing the expression levels of sRNAs before and after infestation, 508 specific sRNAs were significantly up-regulated in Arabidopsis after infestation. In addition, the results show that AI models, including SVM, RF, XGBoost, and CNN using two-dimensional convolution, have robust classification features at the sequence level, with a prediction accuracy of about 96.8%. A comparison of specific sRNAs with genome sequences revealed that 247 matched precisely with the TuYV genome sequence but not with the Arabidopsis genome, suggesting that TuYV viruses may be their source. The 247 sRNAs predicted target genes and enrichment analysis, which identified 206 Arabidopsis genes involved in nine biological processes and three KEGG pathways associated with plant growth and viral stress tolerance, corresponding to 108 sRNAs. These findings provide a reference for studying sRNA-mediated interactions in pathogen infection and are essential for establishing a vital resource of regulation network for the virus infecting plants and deepening the understanding of TuYV virus infection patterns. However, further validation of these sRNAs is needed to gain a new understanding.
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spelling pubmed-98581062023-01-21 Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana Yu, Ruiyang Ye, Xinghuo Zhang, Chenghua Hu, Hailong Kang, Yanlei Li, Zhong Curr Issues Mol Biol Article Virus infestation can seriously harm the host plant’s growth and development. Turnip yellows virus (TuYV) infestation of host plants can cause symptoms, such as yellowing and curling of leaves and root chlorosis. However, the regulatory mechanisms by which TuYV affects host growth and development are unclear. Hence, it is essential to mine small RNA (sRNA) and explore the regulation of sRNAs on plant hosts for disease control. In this study, we analyzed high-throughput data before and after TuYV infestation in Arabidopsis using combined genetics, statistics, and machine learning to identify 108 specifically expressed and critical functional sRNAs after TuYV infection. First, comparing the expression levels of sRNAs before and after infestation, 508 specific sRNAs were significantly up-regulated in Arabidopsis after infestation. In addition, the results show that AI models, including SVM, RF, XGBoost, and CNN using two-dimensional convolution, have robust classification features at the sequence level, with a prediction accuracy of about 96.8%. A comparison of specific sRNAs with genome sequences revealed that 247 matched precisely with the TuYV genome sequence but not with the Arabidopsis genome, suggesting that TuYV viruses may be their source. The 247 sRNAs predicted target genes and enrichment analysis, which identified 206 Arabidopsis genes involved in nine biological processes and three KEGG pathways associated with plant growth and viral stress tolerance, corresponding to 108 sRNAs. These findings provide a reference for studying sRNA-mediated interactions in pathogen infection and are essential for establishing a vital resource of regulation network for the virus infecting plants and deepening the understanding of TuYV virus infection patterns. However, further validation of these sRNAs is needed to gain a new understanding. MDPI 2022-12-30 /pmc/articles/PMC9858106/ /pubmed/36661502 http://dx.doi.org/10.3390/cimb45010016 Text en © 2022 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
Yu, Ruiyang
Ye, Xinghuo
Zhang, Chenghua
Hu, Hailong
Kang, Yanlei
Li, Zhong
Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana
title Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana
title_full Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana
title_fullStr Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana
title_full_unstemmed Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana
title_short Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana
title_sort identification of specific pathogen-infected srna-mediated interactions between turnip yellows virus and arabidopsis thaliana
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9858106/
https://www.ncbi.nlm.nih.gov/pubmed/36661502
http://dx.doi.org/10.3390/cimb45010016
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