Genomics and functional dynamics of effector...

• 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