Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera

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Abstract
Background: Grosmannia clavigerais a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and associated fungi by releasing terpenoid and phenolic defense compounds. It is unclear which genes are important forG. clavigera's ability to overcome antifungal pine terpenoids and phenolics.Results: We constructed seven cDNA libraries from eightG. clavigeraisolates grown under various culture conditions, and Sanger sequenced the 5' and 3' ends of 25,000 cDNA clones, resulting in 44,288 high quality ESTs. The assembled dataset of unique transcripts (unigenes) consists of 6,265 contigs and 2,459 singletons that mapped to 6,467 locations on theG. clavigerareference genome, representing ~70% of the predictedG. clavigeragenes. Although only 54% of the unigenes matched characterized proteins at the NCBI database, this dataset extensively covers major metabolic pathways, cellular processes, and genes necessary for response to environmental stimuli and genetic information processing. Furthermore, we identified genes expressed in spores prior to germination, and genes involved in response to treatment with lodgepole pine phloem extract (LPPE).Conclusions: We provide a comprehensively annotated EST dataset forG. clavigerathat represents a rich resource for gene characterization in this and other ophiostomatoid fungi. Genes expressed in response to LPPE treatment are indicative of fungal oxidative stress response. We identified two clusters of potentially functionally related genes responsive to LPPE treatment. Furthermore, we report a simple method for identifying contig misassemblies inde novoassembled EST collections caused by gene overlap on the genome.