Open Access Highly Accessed Research article

Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae

Vidhyavathi Raman1, Stacey A Simon12, Amanda Romag13, Feray Demirci12, Sandra M Mathioni14, Jixian Zhai12, Blake C Meyers12 and Nicole M Donofrio1*

  • * Corresponding author: Nicole M Donofrio ndonof@udel.edu

  • † Equal contributors

Author Affiliations

1 Department of Plant & Soil Sciences, University of Delaware, Newark, DE, 19716, USA

2 Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA

3 Boyce Thompson Institute, Ithaca, NY, 14853, USA

4 Department of Phytopathology, Federal University of Lavras, Lavras, MG, 37.200-000, Brazil

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BMC Genomics 2013, 14:326  doi:10.1186/1471-2164-14-326

Published: 12 May 2013

Abstract

Background

The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new species of sRNAs have been identified in fungi. This fact along with the availability of genome sequence makes M. oryzae a compelling target for sRNA profiling. We have examined sRNA species and their biosynthetic genes in M. oryzae, and the degree to which these elements regulate fungal stress responses. To this end, we have characterized sRNAs under different physiological stress conditions, which had not yet been examined in this fungus.

Results

The resulting libraries are composed of more than 37 million total genome matched reads mapping to intergenic regions, coding sequences, retrotransposons, inverted, tandem, and other repeated regions of the genome with more than half of the small RNAs arising from intergenic regions. The 24 nucleotide (nt) size class of sRNAs was predominant. A comparison to transcriptional data of M. oryzae undergoing the same physiological stresses indicates that sRNAs play a role in transcriptional regulation for a small subset of genes. Support for this idea comes from generation and characterization of mutants putatively involved in sRNAs biogenesis; our results indicate that the deletion of Dicer-like genes and an RNA-Dependent RNA Polymerase gene increases the transcriptional regulation of this subset of genes, including one involved in virulence.

Conclusions

Various physiological stressors and in planta conditions alter the small RNA profile of the rice blast fungus. Characterization of sRNA biosynthetic mutants helps to clarify the role of sRNAs in transcriptional control.

Keywords:
Small RNA; Magnaporthe oryzae; Rice blast fungus; siRNA