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Open Access Research article

Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi

William Hintz1*, Michael Pinchback1, Paul de la Bastide1, Steven Burgess1, Volker Jacobi2, Richard Hamelin3, Colette Breuil4 and Louis Bernier2

Author Affiliations

1 Biology Department, University of Victoria, P.O. Box 3020 STN CSC, Victoria, BC, V8W 3N5, Canada

2 Centre d'étude de la forêt (CEF), Faculté de foresterie et de géomatique, Université Laval, Québec (Québec) G1K 7P4, Canada

3 Service canadien des forêts, Ressources naturelles Canada, Centre de foresterie des Laurentides, 1055 du PEPS, P.O. Box 3800, Québec (Québec) G1V 4C7 Canada

4 Department of Wood Science, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada

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BMC Genomics 2011, 12:431  doi:10.1186/1471-2164-12-431

Published: 24 August 2011

Abstract

Background

The highly aggressive pathogenic fungus Ophiostoma novo-ulmi continues to be a serious threat to the American elm (Ulmus americana) in North America. Extensive studies have been conducted in North America to understand the mechanisms of virulence of this introduced pathogen and its evolving population structure, with a view to identifying potential strategies for the control of Dutch elm disease. As part of a larger study to examine the genomes of economically important Ophiostoma spp. and the genetic basis of virulence, we have constructed an expressed sequence tag (EST) library using total RNA extracted from the yeast-like growth phase of O. novo-ulmi (isolate H327).

Results

A total of 4,386 readable EST sequences were annotated by determining their closest matches to known or theoretical sequences in public databases by BLASTX analysis. Searches matched 2,093 sequences to entries found in Genbank, including 1,761 matches with known proteins and 332 matches with unknown (hypothetical/predicted) proteins. Known proteins included a collection of 880 unique transcripts which were categorized to obtain a functional profile of the transcriptome and to evaluate physiological function. These assignments yielded 20 primary functional categories (FunCat), the largest including Metabolism (FunCat 01, 20.28% of total), Sub-cellular localization (70, 10.23%), Protein synthesis (12, 10.14%), Transcription (11, 8.27%), Biogenesis of cellular components (42, 8.15%), Cellular transport, facilitation and routes (20, 6.08%), Classification unresolved (98, 5.80%), Cell rescue, defence and virulence (32, 5.31%) and the unclassified category, or known sequences of unknown metabolic function (99, 7.5%). A list of specific transcripts of interest was compiled to initiate an evaluation of their impact upon strain virulence in subsequent studies.

Conclusions

This is the first large-scale study of the O. novo-ulmi transcriptome. The expression profile obtained from the yeast-like growth phase of this species will facilitate a multigenic approach to gene expression studies to assess their role in the determination of pathogenicity for this species. The identification and evaluation of gene targets in such studies will be a prerequisite to the development of biological control strategies for this pathogen.