Oomycetes Overview

2. Oomycete Genomics, Past, Present and Future Brett Tyler Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University

4. Past

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

7. Effector genes are associated with repeat rich regions in oomycete genomes Haas et al (2009) Nature 461(7262): 393-399

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

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

10. Present

12. Future

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

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