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Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs
In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focuse...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804510/ https://www.ncbi.nlm.nih.gov/pubmed/24204767 http://dx.doi.org/10.1371/journal.pone.0077181 |
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author | Fahlgren, Noah Bollmann, Stephanie R. Kasschau, Kristin D. Cuperus, Josh T. Press, Caroline M. Sullivan, Christopher M. Chapman, Elisabeth J. Hoyer, J. Steen Gilbert, Kerrigan B. Grünwald, Niklaus J. Carrington, James C. |
author_facet | Fahlgren, Noah Bollmann, Stephanie R. Kasschau, Kristin D. Cuperus, Josh T. Press, Caroline M. Sullivan, Christopher M. Chapman, Elisabeth J. Hoyer, J. Steen Gilbert, Kerrigan B. Grünwald, Niklaus J. Carrington, James C. |
author_sort | Fahlgren, Noah |
collection | PubMed |
description | In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work. |
format | Online Article Text |
id | pubmed-3804510 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-38045102013-11-07 Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs Fahlgren, Noah Bollmann, Stephanie R. Kasschau, Kristin D. Cuperus, Josh T. Press, Caroline M. Sullivan, Christopher M. Chapman, Elisabeth J. Hoyer, J. Steen Gilbert, Kerrigan B. Grünwald, Niklaus J. Carrington, James C. PLoS One Research Article In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work. Public Library of Science 2013-10-21 /pmc/articles/PMC3804510/ /pubmed/24204767 http://dx.doi.org/10.1371/journal.pone.0077181 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. |
spellingShingle | Research Article Fahlgren, Noah Bollmann, Stephanie R. Kasschau, Kristin D. Cuperus, Josh T. Press, Caroline M. Sullivan, Christopher M. Chapman, Elisabeth J. Hoyer, J. Steen Gilbert, Kerrigan B. Grünwald, Niklaus J. Carrington, James C. Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs |
title |
Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs |
title_full |
Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs |
title_fullStr |
Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs |
title_full_unstemmed |
Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs |
title_short |
Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs |
title_sort | phytophthora have distinct endogenous small rna populations that include short interfering and micrornas |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3804510/ https://www.ncbi.nlm.nih.gov/pubmed/24204767 http://dx.doi.org/10.1371/journal.pone.0077181 |
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