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2012 Bioinformatics workshop

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  • 1. Funding Acknowledgements 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

2. Oomycete Genomics, Past, Present and Future Brett TylerCenter for Genome Research and BiocomputingOregon State University and Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University 3. Some Phytophthora hostsPhytophthoraalfalfalarchGenomealmondapple macadamia melonapricot Sequencingmustardavocadooakazalea oil palmbanana papaya> 120 destructive bean (Phaseolus) passionfruitpathogen speciesblackberry pea (Pisum)blueberrypeachBrassica pearSequenced cabbagepecanIn progress cacaopeppercanola periwinklecantaloupe pinecarnationpineapplecauliflowerpistachiocedarplumchestnut pomegranatechickpea potatocitrus pumpkinclover raspberrycoconutrhododendroncoffee safflowercotton sesamecowpea soybeancranberrysquashcucurbitsstrawberrydate palmsugar beetegg plantsunflowereucalyptus tobaccofirtomatoguavaviburnumhibiscus walnuthops zucchini 4. Some Phytophthora hostsPhytophthora alfalfalarchGenome almond applemacadamiamelon apricot Sequencing mustard avocadooak azalea oil palm banana papaya> 120 destructivebean (Phaseolus) passionfruitpathogen species blackberry pea (Pisum) blueberrypeach Brassica pearSequencedcabbagepecanIn progresscacaopepper canola periwinkleNew initiative with BGIcantaloupe pine(eventually all species) carnationpineapple cauliflowerpistachio cedarplum chestnut pomegranate chickpea potato citrus pumpkin clover raspberry coconutrhododendron coffee safflower cotton sesame cowpea soybean cranberrysquash cucurbitsstrawberry date palmsugar beet egg plantsunflower eucalyptus tobacco firtomato guavaviburnum hibiscus walnut hops zucchini 5. Oomycete 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 6. Conserved gene order within the PeronosporalesHyaloperonosporaarabidopsidisscaffolds 9; 126; 7; 47Baxter et al 2010Phytophthorainfestanssupercontig1.1Haas et al 2009Phytophthora ramorumscaffold_1Tyler et al 2006Pythium ultimumscf1117875581354Levesque et al 2010PHRINGE analysis: Jeff Boore 7. Effector genes are associated with repeat richregions in oomycete genomes Haas et al (2009) Nature 461(7262): 393-399 8. Protein toxin genes have expanded subsequent to speciationthe NPP1 familyCredit: Mark Gijzen Necrosis = death: P. sojae effect of P.sojae NIP P. ramorumQutob et al Plant J. 32, 361, 2002 9. Rapidly diverging RXLR superfamily in Oomycetes median27aa14aa 126aa range10-67aa 7-55aa 28-835aa Signal Peptide RXLR dEERP. sojae ~400P. ramorum ~370P. infestans ~550H. arabidopsidis ~130 Includes 16/17 cloned oomycete avirulence genes PsAvr1a, PsAvr1b, PsAvr1k, PsAvr3a, PsAvr3b, PsAvr3c, PsAvr4/6, PsAvr5 PiAvr1, PiAvr2, PiAvr3a, PiAvr4, PiAvrPlb1/ipiO1, PiAvrPlb2, HaAtr1, HaAtr13Jiang et al PNAS HaAtr5105(12), 4874-4879 (2008) 10. Data, data, everywhere but ...is it knowledge? Even today the ability to generate high throughputsequencing and other omic data is outstripping the abilityto transform the data into knowledge Automated data processing pipelines are not a substitutefor human insight 11. Integration of Oomycete & Fungal Database ResourcesVMDvmd.vbi.vt.eduFungiDBwww.FungiDB.orgDOE JGI Mycocosmhttp://genome.jgi-psf.org/programs/fungi/index.jsf 12. PERL and a PipetmanLife in a data-rich environmentEvery experimental biologist needs to be a computationalbiologist too Theory Experiment Modeling Simulation