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High-throughput sequencing reveals small RNAs involved in ASGV infection
BACKGROUND: Plant small RNAs (sRNAs) associated with virulent virus infections have been reported by previous studies, while the involvement of sRNAs in latent virus infection remains largely uncharacterised. Apple trees show a high degree of resistance and tolerance to viral infections. We analysed...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118050/ https://www.ncbi.nlm.nih.gov/pubmed/24998458 http://dx.doi.org/10.1186/1471-2164-15-568 |
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author | Visser, Marike Maree, Hans J Rees, D Jasper G Burger, Johan T |
author_facet | Visser, Marike Maree, Hans J Rees, D Jasper G Burger, Johan T |
author_sort | Visser, Marike |
collection | PubMed |
description | BACKGROUND: Plant small RNAs (sRNAs) associated with virulent virus infections have been reported by previous studies, while the involvement of sRNAs in latent virus infection remains largely uncharacterised. Apple trees show a high degree of resistance and tolerance to viral infections. We analysed two sRNA deep sequencing datasets, prepared from different RNA size fractions, to identify sRNAs involved in Apple stem grooving virus (ASGV) infection. RESULTS: sRNA analysis revealed virus-derived siRNAs (vsiRNAs) originating from two ASGV genetic variants. A vsiRNA profile for one of the ASGV variants was also generated showing an increase in siRNA production towards the 3′ end of the virus genome. Virus-derived sRNAs longer than those previously analysed were also observed in the sequencing data. Additionally, tRNA-derived sRNAs were identified and characterised. These sRNAs covered a broad size-range and originated from both ends of the mature tRNAs as well as from their central regions. Several tRNA-derived sRNAs showed differential regulation due to ASGV infection. No changes in microRNA, natural-antisense transcript siRNA, phased-siRNA and repeat-associated siRNA levels were observed. CONCLUSIONS: This study is the first report on the apple sRNA-response to virus infection. The results revealed the vsiRNAs profile of an ASGV variant, as well as the alteration of the tRNA-derived sRNA profile in response to latent virus infection. It also highlights the importance of library preparation in the interpretation of high-throughput sequencing data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-568) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4118050 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41180502014-08-05 High-throughput sequencing reveals small RNAs involved in ASGV infection Visser, Marike Maree, Hans J Rees, D Jasper G Burger, Johan T BMC Genomics Research Article BACKGROUND: Plant small RNAs (sRNAs) associated with virulent virus infections have been reported by previous studies, while the involvement of sRNAs in latent virus infection remains largely uncharacterised. Apple trees show a high degree of resistance and tolerance to viral infections. We analysed two sRNA deep sequencing datasets, prepared from different RNA size fractions, to identify sRNAs involved in Apple stem grooving virus (ASGV) infection. RESULTS: sRNA analysis revealed virus-derived siRNAs (vsiRNAs) originating from two ASGV genetic variants. A vsiRNA profile for one of the ASGV variants was also generated showing an increase in siRNA production towards the 3′ end of the virus genome. Virus-derived sRNAs longer than those previously analysed were also observed in the sequencing data. Additionally, tRNA-derived sRNAs were identified and characterised. These sRNAs covered a broad size-range and originated from both ends of the mature tRNAs as well as from their central regions. Several tRNA-derived sRNAs showed differential regulation due to ASGV infection. No changes in microRNA, natural-antisense transcript siRNA, phased-siRNA and repeat-associated siRNA levels were observed. CONCLUSIONS: This study is the first report on the apple sRNA-response to virus infection. The results revealed the vsiRNAs profile of an ASGV variant, as well as the alteration of the tRNA-derived sRNA profile in response to latent virus infection. It also highlights the importance of library preparation in the interpretation of high-throughput sequencing data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-568) contains supplementary material, which is available to authorized users. BioMed Central 2014-07-07 /pmc/articles/PMC4118050/ /pubmed/24998458 http://dx.doi.org/10.1186/1471-2164-15-568 Text en © Visser et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Visser, Marike Maree, Hans J Rees, D Jasper G Burger, Johan T High-throughput sequencing reveals small RNAs involved in ASGV infection |
title | High-throughput sequencing reveals small RNAs involved in ASGV infection |
title_full | High-throughput sequencing reveals small RNAs involved in ASGV infection |
title_fullStr | High-throughput sequencing reveals small RNAs involved in ASGV infection |
title_full_unstemmed | High-throughput sequencing reveals small RNAs involved in ASGV infection |
title_short | High-throughput sequencing reveals small RNAs involved in ASGV infection |
title_sort | high-throughput sequencing reveals small rnas involved in asgv infection |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118050/ https://www.ncbi.nlm.nih.gov/pubmed/24998458 http://dx.doi.org/10.1186/1471-2164-15-568 |
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