• 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
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
Oomycetes and Genome Sequencing
ultimum
plant pathogens
animal pathogens
alfalfaalmondappleapricotavocadoazaleabananabean (Phaseolus)blackberryblueberryBrassicacabbagecacaocanolacantaloupecarnationcauliflowercedarchestnutchickpeacitrusclovercoconutcoffeecottoncowpeacranberrycucurbitsdate palm egg planteucalyptusfirguavahibiscushops
larchmacadamiamelonmustardoakoil palmpapayapassionfruitpea (Pisum)peachpearpecanpepperperiwinklepinepineapplepistachioplumpomegranatepotatopumpkinraspberryrhododendronsafflowersesamesoybeansquashstrawberrysugar beetsunflowertobaccotomatoviburnumwalnutzucchini
PhytophthoraGenome
Sequencing
Some Phytophthora hosts
Sequenced
In progress
> 120 destructive pathogen species
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)
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
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
Effector genes are associated with repeat rich regions in oomycete genomes
Haas et al (2009) Nature 461(7262): 393-399
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
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)
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
