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Genome of First Fungal Pathogen Unveiled

Genome of First Fungal Pathogen Unveiled
Genome of First Fungal Pathogen Unveiled


Duke Health News Duke Health News

DURHAM, N.C. -- Geneticists at the Duke Institute for Genome
Sciences and Policy
(IGSP) and the University of Basel have
unveiled the complete genome sequence of the pathogenic plant
fungus Ashbya gossypii, which infects agricultural crops
including cotton and citrus fruits in the tropics. The fungus
has the smallest genome yet characterized among free-living
eukaryotes. Eukaryotes are the single-celled and multicellular
organisms that include fungi, plants and animals.

The team -- led by Fred Dietrich, Ph.D., of the IGSP's
Center for Genome Technology, and Peter Phillipsen, Ph.D., of the
University of Basel -- reported its findings online in the
March 4, 2004, Science
, the online version of the journal Science. The
work was completed with the funding and collaboration of
Novartis (now Syngenta) in Research Triangle Park, N.C. The
researchers have no financial ties to Novartis or Syngenta.

The sequencing of the fungal genome has already shed light
on the evolution of Saccharomyces cerevisiae -- the
single-celled baker's yeast that scientists rely on for the
study of many basic questions in cell biology. Furthermore,
understanding the infectious microbe's genetic instructions
might allow scientists to tease out the fundamental features
responsible for some fungi's ability to cause disease, the
researchers said.

"We expect many similarities in function among all types of
fungal pathogens -- whether they infect plants or humans," said
Dietrich, first author of the study. "Understanding one will
provide insight into fungal pathogens in general in terms of
the forces that drive them."

Ashbya's stripped-down genome -- containing just 9.2 million
DNA base pairs, the fundamental building blocks of inheritance
-- will further simplify the task of deciphering genes and
their functions, he added. The genomes of other important
fungal pathogens can include as many as 200 million base pairs,
more than 20 times that of the Ashbya genome. In comparison,
the genetic blueprints contained in each human cell run to some
3 billion DNA base pairs.

The researchers first sequenced the Ashbya genome three
times over in many segments and assembled those pieces into the
sequences of the fungus' seven chromosomes. The team then
filled in any remaining gaps in the initial scaffold through
additional sequencing. By comparing the sequence information to
the yeast genome, the investigators identified the location of
genes along the chromosomes.

Ashyba's 9.2 million base pair genome encodes 4,718 protein
coding genes, the team reported. The fungus shares more than 90
percent of those with yeast, with most occurring in a similar
gene order.

Further comparison of the Ashbya and yeast genomes revealed
300 instances of sequence inversion or movement of a segment
from one location to another since the divergence of the two
species. The analysis also revealed two copies of the majority
of Ashbya genes in the yeast genome, evidence that the
evolution of S. cerevisiae included a whole genome

The fully annotated sequence will be made publicly available
on GenBank,
the National Institutes of Health genetic sequence

"This is the culmination of the work of many people over
more than 10 years," said Dietrich. "It's very satisfying to
finally be able to make this data public." The support of
Novartis hinged on an agreement that the data not be made
public until the genome was complete, he said.

Collaborators on the project included Philippe Luedi, of
Duke University Medical Center; Sylvia Voegeli, Sophie Brachat,
Ph.D., Anita Lerch, Sabine Steiner, Ph.D., Christine Mohr,
Ph.D., and Rainer Pohlmann, Ph.D., of the University of Basel;
Krista Gates, Albert Flavier, Ph.D., and Thomas Gaffney, Ph.D.,
of Syngenta Biotechnology in Research Triangle Park; and
Sangdun Choi, Ph.D., and Rod Wing, Ph.D., of Clemson University
in South Carolina.

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