Open Access Research article

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

Uljana Hesse-Orce1, Scott DiGuistini1, Christopher I Keeling2, Ye Wang1, Maria Li2, Hannah Henderson2, T Roderick Docking3, Nancy Y Liao3, Gordon Robertson3, Robert A Holt3, Steven JM Jones3, Jörg Bohlmann2 and Colette Breuil1*

Author Affiliations

1 Department of Wood Science, University of British Columbia, Vancouver, Canada

2 Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

3 BC Cancer Agency Genome Sciences Centre, Vancouver, Canada

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BMC Genomics 2010, 11:536  doi:10.1186/1471-2164-11-536

Published: 4 October 2010

Abstract

Background

Grosmannia clavigera is 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 for G. clavigera's ability to overcome antifungal pine terpenoids and phenolics.

Results

We constructed seven cDNA libraries from eight G. clavigera isolates 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 the G. clavigera reference genome, representing ~70% of the predicted G. clavigera genes. 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 for G. clavigera that 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 in de novo assembled EST collections caused by gene overlap on the genome.