BG Journal Club

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Bioinformatics and Genomics
Journal Club on Phytophthora evolutionary study

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  • Main page of my presentation I’m going to talk about the two databases I’m working on. The first one is Phytophthora Database which initiated in 2006. It’s almost 3 years ago. The second one is Pythium Database, and I made it but it needs lots of effort to Plant Pathogen community make it standard.
  • Here is a taxonomy for Phytophthora and Pythium. They are Oomycetes and Facultative parasites which can be found in soil or water.
  • The genus Phytophthora is closely related to the genus Pythium . Two genera listed in order of the dates of their descriptions : Pythium Pringsheim (1858), Phytophthora de Bary (1876)
  • 2003, the sudden oak death in california destroyed a lot of oak trees. It’s been found that the Phytophthora ramorum was pathogen.
  • Here is the symptoms of Phytophthora ramorum. You can see those pictures in species description page in Phytophthora Database.
  • 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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