title: Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici).
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Molecular Plant Sciences, Washington State University, Pullman, WA, USA. nicholas.mueth@wsu.edu.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Mueth
authors.affiliation: Plant Pathology, Washington State University, Pullman, WA, USA. sowmya.ramachandran@wsu.edu.
authors.forename: Sowmya R
authors.initials: SR
authors.lastname: Ramachandran
authors.affiliation: Molecular Plant Sciences, Washington State University, Pullman, WA, USA. scot_hulbert@wsu.edu.|Plant Pathology, Washington State University, Pullman, WA, USA. scot_hulbert@wsu.edu.
authors.forename: Scot H
authors.initials: SH
authors.lastname: Hulbert
mesh_terms: D001487:Basidiomycota / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D015966:Gene Expression Regulation, Fungal; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D010935:Plant Diseases / Q000382:microbiology; D034622:RNA Interference; D012331:RNA, Fungal; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D034741:RNA, Small Interfering; D017423:Sequence Analysis, RNA; D014908:Triticum / Q000382:microbiology*
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger; D034741:RNA, Small Interfering