Malali Gowda¹ , Venu Reddyvarichannarayappa¹ , Kan Kobuta² , Huizhuan Wu² , Mohan Raghupathy¹ , Chatchawan Jantasuriyarat¹ , Huameng Li¹ , HyeRan Kim³ , Eric Stahlberg⁴ , Rod Wing³ , Sean Couglan⁵ , Christian Haudenschild⁶ , Ralph Dean⁷ , Blake Meyers² , Guo-Liang Wang¹

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

²  University of Delaware, Delaware Biotechnology Institute, Delaware Technology Park, 15 Innovation Way, Newark, DE 19711

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

⁴  Ohio Supercomputer Center, The Ohio State University, Columbus, OH 43212

⁵  Agilent Technologies Inc, Little Falls Site, 2850 Centerville Road, DE 19808

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

⁷  Fungal Genomics Laboratory, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695

Rice blast, caused by the fungal pathogen Magnaporthe grisea, is one of the devastating diseases of rice and causes tremendous yield loss in rice production worldwide. To identify all the expressed genes encoded in the fungal genome, we analyzed the mycelium and appressorium transcriptomes using MPSS, RL-SAGE and oligoarray methods. Unique MPSS tags from mycelia (20,299) and appressoria (16,427) were identified. The two transcriptomes are quite different as there are only about 22.3% of the tags that were present in both libraries. Nearly 85% of the MPSS significant tags from mycelia and appressoria found matches in the M. grisea genome. In the RL-SAGE mycelium library, 51,925 unique tags were identified, of which 64% of the significant tags matched to the genome. About 40% of the tags were novel transcripts from MPSS libraries and 55% of the tags were novel transcripts in RL-SAGE library when the tags matched to the genome sequence were compared with the current EST collections. About 50% of the annotated genes encode an antisense transcript tags. Over 19% of the genes in M. grisea encode both sense and antisense transcripts, which may form double-stranded RNA molecules. In oligoarray analysis, we identified 3,793 mycelium-specific genes and 4,652 appressorium-specific genes. A moderate to good correlation of gene expression patterns was observed between MPSS and oligoarray data. But the correlation between RL-SAGE and MPSS or oligoarray was not significant, probably due to the differences in the tag and probe locations among the annotated genes. Our results demonstrated that MPSS, RL-SAGE and oligoarray are powerful techniques and are complementary to each other for comprehensive transcriptome analysis and genome annotation of complex genomes.