Speaker: Amy J. Powell, Ph.D, Fungal Genomics Laboratory, North Carolina State University
Time: 10am-11am, Thursday, September 13th, 2007
Place: 338 Koshland Hall
Abstract:
The role of differential gene gain and/or loss remains largely unexamined in
the context of fungal pathogenesis, particularly on a genomic scale, despite
its known relevance to virulence in bacteria and viruses. To embark on a
genome-wide analysis, the gene families for eleven sequenced fungal genomes
were inventoried to discern whether patterns of gene duplication, a common
mechanism for gene gain, were distinct in pathogens versus
non-pathogens. This analysis included nine Ascomycete species, and two
Basidiomycete lineages. We developed a semi-automated high-throughput
computational platform, FEGA (Fungal
Evolutionary Genome
Analyses) to facilitate large-scale comparative studies to
explore evolutionary patterns associated with fungal pathogenesis. This
platform is comprised of tools and a database that currently contains gene
family assignments, Gene Ontology (GO)-based annotations, gene co-ordinates, as
well as selection and divergence indices. Our platform was engineered to
facilitate extension. Overall, the distribution of gene family sizes was not
distinct in pathogens, as compared to non-pathogens. However,
phylogenetically informed comparisons revealed several instances where fungal
pathogens showed globally altered patterns of gene duplication, as indicated by
differences in gene family size distribution. Genome-wide surveys of gene
family dynamics revealed eighteen possible examples of gene family expansion,
as well as eight instances of gene family contraction in pathogenic lineages.
Examples of gene families showing expansion in pathogens included those known
to be important in insect exoskeleton or plant host cell wall modification
(e.g., chitin deacetylase, cutin hydrolase, endoglucanase, feruloyl
esterase). Instances of contracted gene families included those with vacuolar
ATP synthase and alcohol dehydrogenase function. Pairwise species comparisons
revealed additional instances of expanded gene families. A survey of the
functional distribution of gene duplicates indicated that pathogens, globally,
showed enrichment for duplicates associated with receptor and hydrolase
activities, and Ascomycete pathogens appear to have not only these
differences, but also significantly more duplicates associated with regulatory
and carbohydrate binding functions. The observed functional differences
possibly have adaptive value for pathogens, and likely reflect ancient, as well
as contemporary intimate associations with a host.
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