Whole Genome Sequencing of Pythium ultimum
Agricultural production is under constant and increasing
pressure
from losses due to plant pathogens. One important and ubiquitous plant
pathogen taxon is the genus Pythium, a fungal-like
organism, which
causes a variety of diseases including seed rots and damping-off, root,
stem and fruit rots, foliar blights and postharvest decay. Pythium spp.
are a major cause of seed rot prior to germination, especially in cold,
poorly drained soils and almost all germinating seed and developing
roots are exposed to infection by Pythium. However,
we currently have
only a limited understanding on the molecular basis of its
pathogenicity. More importantly, plant disease diagnosticians do not
routinely identify Pythium to the species level
because of the
difficulty and time required to produce and identify the morphological
characteristic necessary for speciation. While some Pythium
species can
be differentiated based on sequence differences in the ribosomal RNA
internal transcribed spacer (ITS), in several cases, representative
strains of one species had identical ITS sequences to those of another,
thereby suggesting taxonomic synonymy among certain described species
or the need for multigenic analysis to set species boundaries. The
Amercian Phytopathological Society identified Pythium
as one of the
‘high priority’ plant pathogens for microbial genome sequencing. We
will increase our knowledge of this significant plant pathogen genus by
sequencing and annotating a representative isolate of P.
ultimum. We
will also skim sequence (2X sequence coverage) another strain of P.
ultimum to provide comparative genomic data on this species.
To further
our understanding of the oomycetes, we will perform comparative genome
analyses with our two Pythium isolates and five
other plant pathogenic
oomycete species for which there is (will be) publicly available genome
sequence and annotation data. Through these comparative analyses, we
will be able to further our understanding of not only this important
plant pathogen, but also how to develop more relevant diagnostic
markers that can be used in detecting, controlling the dissemination,
and limiting the impact of this plant pathogen and its relatives. We
will train a graduate student in genomics and bioinformatics and engage
a number of outside scientists, including other graduate students and
postdoctoral fellows, in annotation and comparative genomics of Pythium.
More information about the Pythium Genome Database and the project data can be found on the Pythium Genome Database website: http://pythium.plantbiology.msu.edu/.
