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Published

2012 Bioinformatics workshop

2012 Bioinformatics workshop

Published in Education , Technology
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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 Tyler Center for Genome Research and Biocomputing Oregon State University and Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
  • 3. Some Phytophthora hostsPhytophthora alfalfa larch Genome almond apple macadamia melon apricot Sequencing mustard avocado oak azalea oil palm banana papaya> 120 destructive bean (Phaseolus) passionfruitpathogen species blackberry pea (Pisum) blueberry peach Brassica pear Sequenced cabbage pecan In progress cacao pepper canola periwinkle cantaloupe pine carnation pineapple cauliflower pistachio cedar plum chestnut pomegranate chickpea potato citrus pumpkin clover raspberry coconut rhododendron coffee safflower cotton sesame cowpea soybean cranberry squash cucurbits strawberry date palm sugar beet egg plant sunflower eucalyptus tobacco fir tomato guava viburnum hibiscus walnut hops zucchini
  • 4. Some Phytophthora hostsPhytophthora alfalfa larch Genome almond apple macadamia melon apricot Sequencing mustard avocado oak azalea oil palm banana papaya> 120 destructive bean (Phaseolus) passionfruitpathogen species blackberry pea (Pisum) blueberry peach Brassica pear Sequenced cabbage pecan In progress cacao pepper canola periwinkle New initiative with BGI cantaloupe pine (eventually all species) carnation pineapple cauliflower pistachio cedar plum chestnut pomegranate chickpea potato citrus pumpkin clover raspberry coconut rhododendron coffee safflower cotton sesame cowpea soybean cranberry squash cucurbits strawberry date palm sugar beet egg plant sunflower eucalyptus tobacco fir tomato guava viburnum 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 PeronosporalesHyaloperonospora arabidopsidisscaffolds 9; 126; 7; 47Baxter et al 2010Phytophthora infestanssupercontig1.1Haas et al 2009Phytophthora ramorumscaffold_1Tyler et al 2006Pythium ultimumscf1117875581354Levesque et al 2010 PHRINGE analysis: Jeff Boore
  • 7. Effector genes are associated with repeat rich regions in oomycete genomes Haas et al (2009) Nature 461(7262): 393-399
  • 8. Protein toxin genes have expanded subsequent to speciation the NPP1 family Credit: 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 median 27aa 14aa 126aa range 10-67aa 7-55aa 28-835aa Signal Peptide RXLR dEER P. sojae ~400 P. ramorum ~370 P. infestans ~550 H. 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 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
  • 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 Pipetman Life in a data-rich environmentEvery experimental biologist needs to be a computational biologist too Theory  Experiment Modeling  Simulation