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BG Journal Club

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Bioinformatics and Genomics
Journal Club on Phytophthora evolutionary study

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BG Journal Club

  1. 1. 2009 Fall, BG Journal Club A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences 9/9/2009 Bongsoo Park, Department of Plant Pathology The Pennsylvania State University
  2. 2. Irish Potato Famine (1845-1852)
  3. 3. Courtesy D. Inglis, apsnet.org Potato tuber with late blight Grunwald - Blighted potato field Cochabamba
  4. 4. Tomato leaf and step blight Black/Brown lesions on leaves Water-soaked or chlorotic borders Expanding rapidly and necrotic! www.phytophthoradb.org www.phytophthoradb.org
  5. 5. Disease cycle of late blight of potato and tomato caused by P. infestans Plant Pathology, Agrios, 5ed
  6. 6. A. Sporangiophore; B. Sporangiophore branch showing swellings at successive sites of sporangium formation; C. Sporangia germination by zoospore Figures-Phytophthora Disease Worldwide, 1997, Donald C. Erwin and Olaf K. Ribeiro Sporangiophore and zoospores
  7. 7. Phytophthora genus <ul><li>Taxonomy </li></ul><ul><li>Eukaryota > Chromista (Kingdom)> Oomycota > </li></ul><ul><li>Oomycetes(Class)> Peronosporales > Pythiaceae > Phytophthora </li></ul>Facultative parasites Soil- and water-borne
  8. 8. Father of Plant Pathology Heinrich Anton de Bary (1831-1888) http://en.wikipedia.org/wiki/Heinrich_Anton_de_Bary
  9. 9. Sudden Oak Death (SOD) in CA and OR Phytophthora ramorum Symptoms include bleeding cankers on the tree’s trunk and dieback of the foliage. Sudden Oak Death in California
  10. 10. Tanoak canker Tip necrosis on Rhododendron leaves Ivors, K. http://www.phytophthoradb.org/ Ivors, K. http://www.phytophthoradb.org/ Sudden Oak Death in California
  11. 11. 82 species(Phytophthora) 2 outgroup(Pythium)
  12. 12. Why it is important? 1) Diagnostic and species identification
  13. 13. Why it is important? 1) Diagnostic and species identification 2) Evolutionary history and hypothesis
  14. 14. Why it is important? 1) Diagnostic and species identification 2) Evolutionary history and hypothesis 3) Utilizing available genome sequences Phytophthora Infestans Phytophthora ramorum Phytophthora sojae
  15. 15. Why it is important? 1) Diagnostic and species identification 2) Evolutionary history and hypothesis 3) Utilizing available genome sequences Phytophthora Infestans Phytophthora ramorum Phytophthora sojae 4) Species complex studies initiated.
  16. 16. ITS Regions
  17. 17. ITS Regions Highly conserved region, coding region
  18. 18. ITS Regions Highly conserved region, coding region Variation, Key for diagnostics
  19. 19. COXII Regions
  20. 20. COXII Regions
  21. 21. COXII Regions Example) Phytophthora infestans Phytophthora mirabilis Phytophthora phaseoli
  22. 22. Evolution of Phytophthora B A C D E
  23. 23. More complex, evolutionary questions
  24. 24. More complex, evolutionary questions
  25. 25. More complex, evolutionary questions Using full genome sequences, Alignment, EST sequence
  26. 26. More complex, evolutionary questions Using full genome sequences, Alignment, EST sequence
  27. 27. Criteria for choosing potential markers P. ramorum (66.7Mbp) P. sojae (86.0Mbp) High similarity coding regions Regions of lower similarity or Predicted Introns Similarity to ORF in other eukaryotes Presence of corresponding EST sequences Full genome sequence in 2006 at JGI
  28. 28. 229 72 27 7 Potential Informative Homologous from other eukaryotes Regions of high conservation identified Primer design Criteria for choosing potential markers Tested by PCR
  29. 29. More loci, More accurate? (82+2) * (1+7) = 672 672 * 2 = 1,344 (sequences) What is hypothesis on this? 8,700 nucleotide sites 60S B-tublin Enolase Heat shock protein Large subunit TigA Ef-1a
  30. 30. DNA amplification and sequencing http://www.phytophthoradb.org
  31. 31. Phylogenetic analyses and programs 7 loci sequences Multiple sequence alignment with clustalX Preliminary phylogenetic tree using NJ with a Kimura two parameter nucleotide substitution model Modeltest, Akaike Information Criterion, GARLI Flat Dirichlet, Tracer version, BEAST Alternative topological hypotheses in PAML Maximum Likelihood Maximum Parsimony Bayesian Analyses PAUP, PHYLIP MrBayes
  32. 32. Result
  33. 33. Result
  34. 34. Result
  35. 35. Phytophthora Database Global Phytophthora Network Plant Pathogen Database and Genomic Initiative at Penn State University since 2005 Thank you.

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