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

Vidhyavathi Raman,Feray Demirci,Nicole M Donofrio,Sandra M Mathioni,Blake C Meyers,Jixian Zhai,Stacey A Simon,Amanda Romag

doi:10.1186/1471-2164-14-326

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsVarious 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.

Highlights

The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide
We examined small RNA profiles of M. oryzae during stress conditions matching those of Mathioni et al [29], namely, nitrogen starvation, carbon starvation, minimal media, and paraquat-induced oxidative stress
Small RNA profiling of M. oryzae stress libraries We analyzed small RNA size profiles of libraries constructed from M. oryzae mycelial tissue, and from susceptible rice leaves infected with M. oryzae at two time-points

Summary

Introduction

The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. 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. RNA silencing, the RNA-mediated suppression of a target gene in a sequence specific manner, has been described in many organisms as post-transcriptional gene silencing, RNA interference, and quelling, in plants, animals, and fungi, respectively [1,2]. These silencing pathways are involved in transposon silencing, viral defense, DNA elimination, heterochromatin formation, and post-transcriptional repression of cellular. Appressoria generate enormous amounts of turgor pressure to penetrate the outer surface of the plant, which is followed by tissue invasion and colonization resulting in disease lesions [8]

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