Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici).

Nicholas A Mueth,Scot H Hulbert,Sowmya R Ramachandran

doi:10.1186/s12864-015-1895-4

Abstract

BackgroundWheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. This sophisticated biotrophic parasite infiltrates wheat leaves and develops infection structures inside host cells, appropriating nutrients while suppressing the plant defense response. Development in most eukaryotes is regulated by small RNA molecules, and the success of host-induced gene silencing technology in Puccinia spp. implies the existence of a functional RNAi system. However, some fungi lack this capability, and small RNAs have not yet been reported in rust fungi. The objective of this study was to determine whether P. striiformis carries an endogenous small RNA repertoire.ResultsWe extracted small RNA from rust-infected wheat flag leaves and performed high-throughput sequencing. Two wheat cultivars were analyzed: one is susceptible; the other displays partial high-temperature adult plant resistance. Fungal-specific reads were identified by mapping to the P. striiformis draft genome and removing reads present in uninfected control libraries. Sequencing and bioinformatics results were verified by RT-PCR. Like other RNAi-equipped fungi, P. striiformis produces large numbers of 20–22 nt sequences with a preference for uracil at the 5′ position. Precise post-transcriptional processing and high accumulation of specific sRNA sequences were observed. Some predicted sRNA precursors possess a microRNA-like stem-loop secondary structure; others originate from much longer inverted repeats containing gene sequences. Finally, sRNA-target prediction algorithms were used to obtain a list of putative gene targets in both organisms. Predicted fungal target genes were enriched for kinases and small secreted proteins, while the list of wheat targets included homologs of known plant resistance genes.ConclusionsThis work provides an inventory of small RNAs endogenous to an important plant pathogen, enabling further exploration of gene regulation on both sides of the host/parasite interaction. We conclude that small RNAs are likely to play a role in regulating the complex developmental processes involved in stripe rust pathogenicity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1895-4) contains supplementary material, which is available to authorized users.

Highlights

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses
Fully-emerged flag leaves on 6 week-old wheat plants were inoculated with either PST-100 spores mixed with talcum powder, or mock-inoculated with talcum powder only
Flag leaf tissue was collected for RNA extraction at four days post-inoculation

Summary

Introduction

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. Tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. Wheat stripe rust, caused by Puccinia striiformis f. This sophisticated biotrophic parasite infiltrates wheat leaves and develops infection structures inside host cells, appropriating nutrients while suppressing the plant defense response. Tritici (Pst) is a Basidiomycete fungus that causes wheat stripe rust disease. P. striiformis is an obligate biotroph; the fungus produces specialized infection structures called haustoria inside living host cells [5]. Effector proteins block induction of the plant resistance response, or protect fungal cells from its effects [7]. Using the latest Pst draft genome and transcriptome, genes coding for proteins with effector-like amino acid sequences were identified for further analysis [9, 10]

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