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National Science Foundation Research Coordination Networks in Biology Oomycete Genomics Research Collaboration Network – 2007-2012 USDA CSREES Microbial Genome Sequencing Program Phytophthora parasitica Genome Sequence – 2010-2013 USDA NIFA Oomycete Coordinated Agricultural Project Integrated management of oomycete diseases of soybean and other crop plants – 2011-2016 Funding Acknowledgements

Tyler presentation

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2012 Bioinformatics workshop

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Page 1: Tyler presentation

• National Science Foundation

– Research Coordination Networks in Biology

– Oomycete Genomics Research Collaboration Network

– 2007-2012

• USDA CSREES

– Microbial Genome Sequencing Program

– Phytophthora parasitica Genome Sequence

– 2010-2013

• 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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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)

Page 5: Tyler presentation

Oomycete Genome ComparisonsOomycete Genome Comparisons

• P. sojae vs P.ramorum vs P. infestans– ~9,800 orthologs

– 45-55% of genome orthologous

– 25-45% in recognizable gene families

– ~10% unique

• H. arabidopsidis– ~4400 orthologs

– most gene families smaller

– some genes missing

• zoospore function

• inorganic sulfur and nitrogen assimilation

• P. sojae vs P.ramorum vs P. infestans– ~9,800 orthologs

– 45-55% of genome orthologous

– 25-45% in recognizable gene families

– ~10% unique

• H. arabidopsidis– ~4400 orthologs

– most gene families smaller

– some genes missing

• zoospore function

• inorganic sulfur and nitrogen assimilation

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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 NIPNecrosis = 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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Data, data, everywhere but ...

is it knowledge?

Even today the ability to generate high throughput

sequencing and other “omic” data is outstripping the ability

to transform the data into knowledge

Automated data processing pipelines are not a substitute

for human insight

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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

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Theory Experiment

Modeling Simulation

PERL and a Pipetman Life in a data-rich environment

Every experimental biologist needs to be a computational biologist too