Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi
Date
2011-08-24
Authors
Hintz, William E.
Pinchback, Michael
De la Bastide, Paul
Burgess, Steven
Jacobi, Volker
Hamelin, Richard
Breuil, Colette
Bernier, Louis
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
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), Subcellular
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.
Description
BioMed Central
Keywords
Centre for Forest Biology
Citation
Hintz et al.: Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi. BMC Genomics 2011 12:431.