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

BMC Genomics

Research Article

Thomas K Mitchell¹  Joshua Sailsbery²  YeonYee Oh²  Ralph A Dean²  Douglas E Brown²  Cristiano C Nunes²  Minfeng Xue³  Malali Gowda⁴  Feng Chen⁵ 

[1] Department of Plant Pathology, The Ohio State University, 43210, Columbus, OH, USA;Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, 27606, Raleigh, NC, USA;Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, 27606, Raleigh, NC, USA;Department of Plant Pathology, China Agricultural University, 1000193, Beijing, China;Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, 27606, Raleigh, NC, USA;Next-Generation Genomics Laboratory, Center for Cellular and Molecular Platform, NCBS-GKVK Campus, 560065, Bangalore, India;US DOE Joint Genome Institute, 94598, Walnut Creek, CA, USA;

关键词: Small RNAs;    Posttranscriptional Modification;    Appressorium Formation;    Mature tRNA;    tRNA Locus;   

DOI  :  10.1186/1471-2164-12-288

 received in 2011-02-11, accepted in 2011-06-02,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundEmerging 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.ResultsHere, 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.ConclusionsOur 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.

【 授权许可】

Unknown   
© Nunes et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.