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Oomycetes Overview

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  1. 1. Funding Acknowledgements <ul><li>National Science Foundation </li></ul><ul><ul><li>Research Coordination Networks in Biology </li></ul></ul><ul><ul><li>Oomycete Genomics Research Collaboration Network </li></ul></ul><ul><ul><li>2007-2012 </li></ul></ul><ul><li>USDA CSREES and NSF </li></ul><ul><ul><li>Microbial Genome Sequencing Program </li></ul></ul><ul><ul><li>Finishing the P. sojae Genome Sequence </li></ul></ul><ul><ul><li>2007-2011 </li></ul></ul><ul><li>USDA NIFA </li></ul><ul><ul><li>Oomycete Coordinated Agricultural Project </li></ul></ul><ul><ul><li>Integrated management of oomycete diseases of soybean and other crop plants </li></ul></ul><ul><ul><li>2011-2016 </li></ul></ul>
  2. 2. Oomycete Genomics, Past, Present and Future Brett Tyler Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
  3. 4. Past
  4. 5. Oomycete Genome Comparisons <ul><li>P. sojae vs P.ramorum vs P. infestans </li></ul><ul><ul><li>~9,800 orthologs </li></ul></ul><ul><ul><li>45-55% of genome orthologous </li></ul></ul><ul><ul><li>25-45% in recognizable gene families </li></ul></ul><ul><ul><li>~10% unique </li></ul></ul><ul><li>H. arabidopsidis </li></ul><ul><ul><li>~4400 orthologs </li></ul></ul><ul><ul><li>most gene families smaller </li></ul></ul><ul><ul><li>some genes missing </li></ul></ul><ul><ul><ul><li>zoospore function </li></ul></ul></ul><ul><ul><ul><li>inorganic sulfur and nitrogen assimilation </li></ul></ul></ul>
  5. 6. Conserved gene order within the Peronosporales Phytophthora infestans supercontig1.1 Haas et al 2009 Pythium ultimum scf1117875581354 Levesque et al 2010 Hyaloperonospora arabidopsidis scaffolds 9; 126; 7; 47 Baxter et al 2010 Phytophthora ramorum scaffold_1 Tyler et al 2006 PHRINGE analysis: Jeff Boore
  6. 7. Effector genes are associated with repeat rich regions in oomycete genomes Haas et al (2009) Nature 461(7262): 393-399
  7. 8. 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. sojae P. ramorum
  8. 9. Rapidly diverging RXLR superfamily in Oomycetes 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, HaAtr13 HaAtr5 Jiang et al PNAS 105(12), 4874-4879 (2008) Signal Peptide RXLR dEER 27aa 10-67aa 14aa 7-55aa 126aa 28-835aa median range
  9. 10. Present
  10. 11. Finishing of the P. sojae Genome Sequence <ul><li>New 25X BAC library with 150 kb inserts; fully end-sequenced </li></ul><ul><li>New assembly using Arachne and BAC data </li></ul><ul><li>454 sequencing of three more genotypes of P. sojae </li></ul><ul><li>Genetic mapping with SNPs to join physical and genetic maps </li></ul><ul><li>Automated gap-filling and sequence improvement </li></ul><ul><li>Targeted finishing of BACs using primer walking and transposon insertion </li></ul><ul><li>100m ABI Solid™ RNA sequence tags (75 nt) </li></ul><ul><li>New annotation utilizing RNA seq data and manual annotations from v1.0 </li></ul><ul><ul><li>8000 new genes </li></ul></ul><ul><li>Upgrades to VMD browser </li></ul><ul><li>Undergraduate bioinformatics network </li></ul>Hudson Alpha Institute; DOE JGI; Texas A&M; VBI
  11. 12. Future
  12. 13. Rapid improvement in sequencing capacity <ul><li>Sanger sequencing with Megabace </li></ul><ul><ul><li>$1000/1 Mb raw sequence </li></ul></ul><ul><ul><li>1 machine -> 1 Mb/day </li></ul></ul><ul><ul><li>800-900 bp per read </li></ul></ul><ul><li>454 Life Sciences Pyrosequencing </li></ul><ul><ul><li>$30/1 Mb raw sequence </li></ul></ul><ul><ul><li>1 machine (Titanium) -> 1 Gb/day </li></ul></ul><ul><ul><li>400-500 bp per read </li></ul></ul><ul><li>Illumina bead sequencing; ABI SOLID </li></ul><ul><ul><li>$0.11/1 Mb raw sequence </li></ul></ul><ul><ul><li>1 machine -> 25 Gb/day (HiSeq 2000) </li></ul></ul><ul><ul><li>50-100 bp per read </li></ul></ul><ul><li>Pacific Biosciences </li></ul><ul><ul><li>upcoming single molecule sequencing technology </li></ul></ul><ul><ul><li>$0.03/1 Mb raw sequence? ($1000 human genome) </li></ul></ul><ul><ul><li>1000-10,000 bp/ read? </li></ul></ul>P. sojae 9x 2003 $1.34m P. sojae 9x 2009 $25,000
  13. 14. alfalfa almond apple apricot avocado azalea banana bean (Phaseolus) blackberry blueberry Brassica cabbage cacao canola cantaloupe carnation cauliflower cedar chestnut chickpea citrus clover coconut coffee cotton cowpea cranberry cucurbits date palm egg plant eucalyptus fir guava hibiscus hops larch macadamia melon mustard oak oil palm papaya passionfruit pea (Pisum) peach pear pecan pepper periwinkle pine pineapple pistachio plum pomegranate potato pumpkin raspberry rhododendron safflower sesame soybean squash strawberry sugar beet sunflower tobacco tomato viburnum walnut zucchini Phytophthora Genome Sequencing Some Phytophthora hosts > 120 destructive pathogen species Sequenced In progress
  14. 15. Integration of Oomycete & Fungal Database Resources VMD vmd.vbi.vt.edu FungiDB www.FungiDB.org DOE JGI Mycocosm http://genome.jgi-psf.org/programs/fungi/index.jsf

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