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Open Access Highly Accessed Research article

Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

Cristiano C Nunes1, Malali Gowda12, Joshua Sailsbery1, Minfeng Xue13, Feng Chen4, Douglas E Brown1, YeonYee Oh1, Thomas K Mitchell5 and Ralph A Dean1*

Author Affiliations

1 Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA

2 Next-Generation Genomics Laboratory, Center for Cellular and Molecular Platform, NCBS-GKVK Campus, Bangalore 560065, India

3 Department of Plant Pathology, China Agricultural University, Beijing 1000193, China

4 US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

5 Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA

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BMC Genomics 2011, 12:288  doi:10.1186/1471-2164-12-288

Published: 2 June 2011

Abstract

Background

Emerging knowledge of the impact of small RNAs as important cellular regulators has prompted an explosion of small transcriptome sequencing projects. Although significant progress has been made towards small RNA discovery and biogenesis in higher eukaryotes and other model organisms, knowledge in simple eukaryotes such as filamentous fungi remains limited.

Results

Here, we used 454 pyrosequencing to present a detailed analysis of the small RNA transcriptome (~ 15 - 40 nucleotides in length) from mycelia and appressoria tissues of the rice blast fungal pathogen, Magnaporthe oryzae. Small RNAs mapped to numerous nuclear and mitochondrial genomic features including repetitive elements, tRNA loci, rRNAs, protein coding genes, snRNAs and intergenic regions. For most elements, small RNAs mapped primarily to the sense strand with the exception of repetitive elements to which small RNAs mapped in the sense and antisense orientation in near equal proportions. Inspection of the small RNAs revealed a preference for U and suppression of C at position 1, particularly for antisense mapping small RNAs. In the mycelia library, small RNAs of the size 18 - 23 nt were enriched for intergenic regions and repetitive elements. Small RNAs mapping to LTR retrotransposons were classified as LTR retrotransposon-siRNAs (LTR-siRNAs). Conversely, the appressoria library had a greater proportion of 28 - 35 nt small RNAs mapping to tRNA loci, and were classified as tRNA-derived RNA fragments (tRFs). LTR-siRNAs and tRFs were independently validated by 3' RACE PCR and northern blots, respectively.

Conclusions

Our findings suggest M. oryzae small RNAs differentially accumulate in vegetative and specialized-infection tissues and may play an active role in genome integrity and regulating growth and development.