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• National Science Foundation
– Research Coordination Networks in Biology
– Oomycete Genomics Research Collaboration Network
– 2007-2013
• USDA NIFA
– Oomycete Coordinated Agricultural Project
– Integrated management of oomycete diseases of soybean and other crop plants
– 2011-2016
Funding Acknowledgements
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Oomycete Genomics, Past, Present and Future
Brett Tyler
Center for Genome Research and BiocomputingOregon State University
and
Virginia Bioinformatics InstituteVirginia Polytechnic Institute and State University
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Oomycetes and Genome Sequencing
ultimum
plant pathogens
animal pathogens
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alfalfaalmondappleapricotavocadoazaleabananabean (Phaseolus)blackberryblueberryBrassicacabbagecacaocanolacantaloupecarnationcauliflowercedarchestnutchickpeacitrusclovercoconutcoffeecottoncowpeacranberrycucurbitsdate palm egg planteucalyptusfirguavahibiscushops
larchmacadamiamelonmustardoakoil palmpapayapassionfruitpea (Pisum)peachpearpecanpepperperiwinklepinepineapplepistachioplumpomegranatepotatopumpkinraspberryrhododendronsafflowersesamesoybeansquashstrawberrysugar beetsunflowertobaccotomatoviburnumwalnutzucchini
PhytophthoraGenome
Sequencing
Some Phytophthora hosts
Sequenced
In progress
> 120 destructive pathogen species
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alfalfaalmondappleapricotavocadoazaleabananabean (Phaseolus)blackberryblueberryBrassicacabbagecacaocanolacantaloupecarnationcauliflowercedarchestnutchickpeacitrusclovercoconutcoffeecottoncowpeacranberrycucurbitsdate palm egg planteucalyptusfirguavahibiscushops
larchmacadamiamelonmustardoakoil palmpapayapassionfruitpea (Pisum)peachpearpecanpepperperiwinklepinepineapplepistachioplumpomegranatepotatopumpkinraspberryrhododendronsafflowersesamesoybeansquashstrawberrysugar beetsunflowertobaccotomatoviburnumwalnutzucchini
PhytophthoraGenome
Sequencing
Some Phytophthora hosts
Sequenced
In progress
> 120 destructive pathogen species
New initiative with BGI(eventually all species)
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Oomycete Genome Comparisons
• P. sojae vs P.ramorum vs P. infestans– ~9,800 orthologs (highly conserved genes with same functions)
– 45-55% of genome orthologous
– 25-45% in recognizable gene families
– ~10% unique
– many genes for attacking plant tissue
• Saprolegnia parasitica– ~8400 orthologs
– many more introns
– more compact genome, fewer repetitive sequences
– many genes for attacking animal tissues
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Conserved gene order within the Peronosporales
Phytophthora infestanssupercontig1.1Haas et al 2009
Pythium ultimum
scf1117875581354
Levesque et al 2010
Hyaloperonospora arabidopsidisscaffolds 9; 126; 7; 47Baxter et al 2010
Phytophthora ramorumscaffold_1Tyler et al 2006
PHRINGE analysis: Jeff Boore
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Effector genes are associated with repeat rich regions in oomycete genomes
Haas et al (2009) Nature 461(7262): 393-399
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Necrosis = death: effect of P.sojae NIP
Protein toxin genes have expanded subsequent to speciation the NPP1 family Credit: Mark Gijzen
Qutob et al Plant J. 32, 361, 2002
P. sojaeP. ramorum
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Rapidly diverging RXLR superfamily in Oomycetes
P. sojae ~400P. ramorum ~370P. infestans ~550H. arabidopsidis ~130
Signal Peptide RXLR dEER
27aa10-67aa
14aa7-55aa
126aa28-835aa
medianrange
Includes 16/17 cloned oomycete avirulence genesPsAvr1a, PsAvr1b, PsAvr1k, PsAvr3a,PsAvr3b, PsAvr3c, PsAvr4/6, PsAvr5PiAvr1, PiAvr2,PiAvr3a, PiAvr4, PiAvrPlb1/ipiO1, PiAvrPlb2, HaAtr1, HaAtr13HaAtr5Jiang et al PNAS
105(12), 4874-4879 (2008)
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Integration of Oomycete & Fungal Database Resources
FungiDB
www.FungiDB.org
DOE JGI Mycocosm
http://genome.jgi-psf.org/programs/fungi/index.jsf
VMD vmd.vbi.vt.edu
EumicrobeDB.org