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.

doi:10.1371/journal.pone.0077181

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

Journal Article · Mon Oct 21 00:00:00 EDT 2013 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0077181· OSTI ID:1627645

Fahlgren, Noah ^[1]; Bollmann, Stephanie R. ^[2]; Kasschau, Kristin D. ^[3]; Cuperus, Josh T. ^[3]; Press, Caroline M. ^[2]; Sullivan, Christopher M. ^[3]; Chapman, Elisabeth J. ^[3]; Hoyer, J. Steen ^[4]; Gilbert, Kerrigan B. ^[4]; Grünwald, Niklaus J. ^[2]; Carrington, James C. ^[5]

Donald Danforth Plant Science Center, St. Louis, MO (United States); Oregon State University, Corvallis, OR (United States); DOE/OSTI
US Department of Agriculture (USDA)., Corvallis, OR (United States)
Oregon State University, Corvallis, OR (United States)
Donald Danforth Plant Science Center, St. Louis, MO (United States)
Donald Danforth Plant Science Center, St. Louis, MO (United States); Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology. Center for Genome Research and Biocomputing

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 RNAgenerating 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.

View Accepted Manuscript (DOE)

Research Organization:: Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Research Initiative Competitive Grants Program; USDA National Institute of Food and Agriculture; US Forest Service Pacific Southwest Research Station Sudden Oak Death; National Science Foundation (NSF); National Institutes of Health (NIH)

OSTI ID:: 1627645

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 10 Vol. 8; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
RNA sequencing
double standard RNA
genetic loci
genomics
microRNA's
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small interfering RNA
transposable elements

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

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