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Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum
Phased small interfering RNAs (phasiRNAs) are encoded by a novel class of genes known as phasiRNA producing (PHAS) genes. These genes play important regulatory roles by targeting protein coding transcripts in plant species. In this study, 91 regions were identified as potential PHAS loci in tomato,...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465084/ https://www.ncbi.nlm.nih.gov/pubmed/28596514 http://dx.doi.org/10.1038/s41598-017-02233-x |
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author | Wu, Fangli Chen, Yue Tian, Xing Zhu, Xiaole Jin, Weibo |
author_facet | Wu, Fangli Chen, Yue Tian, Xing Zhu, Xiaole Jin, Weibo |
author_sort | Wu, Fangli |
collection | PubMed |
description | Phased small interfering RNAs (phasiRNAs) are encoded by a novel class of genes known as phasiRNA producing (PHAS) genes. These genes play important regulatory roles by targeting protein coding transcripts in plant species. In this study, 91 regions were identified as potential PHAS loci in tomato, with additional evidence that seven of them can be triggered by five miRNAs. Among the identified loci, 51 were located in genic regions, and the remaining 40 were located in intergenic regions. The transient overexpression of PHAS15 and PHAS26 demonstrated that phasiRNAs predicted by PhaseTank were indeed generated from their respective PHAS loci. Using sRNA-seq data from B. cinerea-infected tomato leaves, we identified 50 B. cinerea-responsive phasiRNAs with increased abundance and five with decreased abundance. Moreover, 164 targets of these differentially expressed phasiRNAs were predicted, and 94 of them were confirmed experimentally using degradome data. Gene ontology analysis of the targets revealed an enrichment of genes with functions related to defense responses and signaling regulation. These results suggest that a large number of endogenous siRNAs, such as phasiRNAs, have not yet been identified in tomato and underscore the urgent need to systematically identify and functionally analyze siRNAs in tomato. |
format | Online Article Text |
id | pubmed-5465084 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-54650842017-06-14 Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum Wu, Fangli Chen, Yue Tian, Xing Zhu, Xiaole Jin, Weibo Sci Rep Article Phased small interfering RNAs (phasiRNAs) are encoded by a novel class of genes known as phasiRNA producing (PHAS) genes. These genes play important regulatory roles by targeting protein coding transcripts in plant species. In this study, 91 regions were identified as potential PHAS loci in tomato, with additional evidence that seven of them can be triggered by five miRNAs. Among the identified loci, 51 were located in genic regions, and the remaining 40 were located in intergenic regions. The transient overexpression of PHAS15 and PHAS26 demonstrated that phasiRNAs predicted by PhaseTank were indeed generated from their respective PHAS loci. Using sRNA-seq data from B. cinerea-infected tomato leaves, we identified 50 B. cinerea-responsive phasiRNAs with increased abundance and five with decreased abundance. Moreover, 164 targets of these differentially expressed phasiRNAs were predicted, and 94 of them were confirmed experimentally using degradome data. Gene ontology analysis of the targets revealed an enrichment of genes with functions related to defense responses and signaling regulation. These results suggest that a large number of endogenous siRNAs, such as phasiRNAs, have not yet been identified in tomato and underscore the urgent need to systematically identify and functionally analyze siRNAs in tomato. Nature Publishing Group UK 2017-06-08 /pmc/articles/PMC5465084/ /pubmed/28596514 http://dx.doi.org/10.1038/s41598-017-02233-x Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Wu, Fangli Chen, Yue Tian, Xing Zhu, Xiaole Jin, Weibo Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum |
title | Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum |
title_full | Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum |
title_fullStr | Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum |
title_full_unstemmed | Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum |
title_short | Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum |
title_sort | genome-wide identification and characterization of phased small interfering rna genes in response to botrytis cinerea infection in solanum lycopersicum |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465084/ https://www.ncbi.nlm.nih.gov/pubmed/28596514 http://dx.doi.org/10.1038/s41598-017-02233-x |
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