• National Science Foundation

– Research Coordination Networks in Biology

– Oomycete Genomics Research Collaboration Network

– 2007-2012

• USDA CSREES and NSF

– Microbial Genome Sequencing Program

– Finishing the P. sojae Genome Sequence

– 2007-2011

• 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

Virginia Bioinformatics InstituteVirginia Polytechnic Institute and State University

Past

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

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 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

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)

Present

• New 25X BAC library with 150 kb inserts; fully end-sequenced• New assembly using Arachne and BAC data• 454 sequencing of three more genotypes of P. sojae• Genetic mapping with SNPs to join physical and genetic maps• Automated gap-filling and sequence improvement• Targeted finishing of BACs using primer walking and transposon

insertion• 100m ABI Solid™ RNA sequence tags (75 nt)• New annotation utilizing RNA seq data and manual annotations

from v1.0• 8000 new genes

• Upgrades to VMD browser• Undergraduate bioinformatics network

Finishing of the P. sojae Genome Sequence

Hudson Alpha Institute; DOE JGI; Texas A&M; VBI

Future

• Sanger sequencing with Megabace

– $1000/1 Mb raw sequence– 1 machine -> 1 Mb/day– 800-900 bp per read

• 454 Life Sciences Pyrosequencing

– $30/1 Mb raw sequence– 1 machine (Titanium) -> 1 Gb/day– 400-500 bp per read

• Illumina bead sequencing; ABI SOLID

– $0.11/1 Mb raw sequence– 1 machine -> 25 Gb/day (HiSeq 2000)– 50-100 bp per read

• Pacific Biosciences

– upcoming single molecule sequencing technology– $0.03/1 Mb raw sequence? ($1000 human genome)– 1000-10,000 bp/ read?

Rapid improvement in sequencing capacity

P. sojae 9x2003 $1.34mP. sojae 9x2003 $1.34m

P. sojae 9x2009 $25,000P. sojae 9x2009 $25,000

alfalfaalmondappleapricotavocadoazaleabananabean (Phaseolus)blackberryblueberryBrassicacabbagecacaocanolacantaloupecarnationcauliflowercedarchestnutchickpeacitrusclovercoconutcoffeecottoncowpeacranberrycucurbitsdate palm egg planteucalyptusfirguavahibiscushops

larchmacadamiamelonmustardoakoil palmpapayapassionfruitpea (Pisum)peachpearpecanpepperperiwinklepinepineapplepistachioplumpomegranatepotatopumpkinraspberryrhododendronsafflowersesamesoybeansquashstrawberrysugar beetsunflowertobaccotomatoviburnumwalnutzucchini

PhytophthoraGenome

Sequencing

Some Phytophthora hosts

Sequenced

In progress

> 120 destructive pathogen species

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