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Open Access Research article

Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods

Malali Gowda1, RC Venu1, Mohan B Raghupathy1, Kan Nobuta2, Huameng Li1, Rod Wing3, Eric Stahlberg4, Sean Couglan5, Christian D Haudenschild6, Ralph Dean7, Baek-Hie Nahm8, Blake C Meyers2* and Guo-Liang Wang1*

Author Affiliations

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

2 Department of Plant and Soil Sciences, University of Delaware, DE 19711, USA

3 Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA

4 Ohio Supercomputer Center, The Ohio State University, Columbus, OH 43210, USA

5 Agilent Technologies Inc, Little Falls Site, 2850 Centerville Road, Delaware 19711, USA

6 Solexa, Inc. 25861 Industrial Blvd, Hayward, CA, 94545, USA

7 Fungal Genomics Laboratory, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA

8 Department of Biological Science, Myongji University, Kyonggido, 449728, Korea

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BMC Genomics 2006, 7:310  doi:10.1186/1471-2164-7-310

Published: 8 December 2006

Abstract

Background

Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants at the transcriptome level. To identify all the expressed genes encoded in the fungal genome, we have analyzed the mycelium and appressorium transcriptomes using massively parallel signature sequencing (MPSS), robust-long serial analysis of gene expression (RL-SAGE) and oligoarray methods.

Results

The MPSS analyses identified 12,531 and 12,927 distinct significant tags from mycelia and appressoria, respectively, while the RL-SAGE analysis identified 16,580 distinct significant tags from the mycelial library. When matching these 12,531 mycelial and 12,927 appressorial significant tags to the annotated CDS, 500 bp upstream and 500 bp downstream of CDS, 6,735 unique genes in mycelia and 7,686 unique genes in appressoria were identified. A total of 7,135 mycelium-specific and 7,531 appressorium-specific significant MPSS tags were identified, which correspond to 2,088 and 1,784 annotated genes, respectively, when matching to the same set of reference sequences. Nearly 85% of the significant MPSS tags from mycelia and appressoria and 65% of the significant tags from the RL-SAGE mycelium library matched to the M. grisea genome. MPSS and RL-SAGE methods supported the expression of more than 9,000 genes, representing over 80% of the predicted genes in M. grisea. About 40% of the MPSS tags and 55% of the RL-SAGE tags represent novel transcripts since they had no matches in the existing M. grisea EST collections. Over 19% of the annotated genes were found to produce both sense and antisense tags in the protein-coding region. The oligoarray analysis identified the expression of 3,793 mycelium-specific and 4,652 appressorium-specific genes. A total of 2,430 mycelial genes and 1,886 appressorial genes were identified by both MPSS and oligoarray.

Conclusion

The comprehensive and deep transcriptome analysis by MPSS and RL-SAGE methods identified many novel sense and antisense transcripts in the M. grisea genome at two important growth stages. The differentially expressed transcripts that were identified, especially those specifically expressed in appressoria, represent a genomic resource useful for gaining a better understanding of the molecular basis of M. grisea pathogenicity. Further analysis of the novel antisense transcripts will provide new insights into the regulation and function of these genes in fungal growth, development and pathogenesis in the host plants.