Bioinformatics and Genomics Journal Club on Phytophthora evolutionary study

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. Irish Potato Famine (1845-1852)

3. Courtesy D. Inglis, apsnet.org Potato tuber with late blight Grunwald - Blighted potato field Cochabamba

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. Disease cycle of late blight of potato and tomato caused by P. infestans Plant Pathology, Agrios, 5ed

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

8. Father of Plant Pathology Heinrich Anton de Bary (1831-1888) http://en.wikipedia.org/wiki/Heinrich_Anton_de_Bary

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. 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. 82 species(Phytophthora) 2 outgroup(Pythium)

12. Why it is important? 1) Diagnostic and species identification

13. Why it is important? 1) Diagnostic and species identification 2) Evolutionary history and hypothesis

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. 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. ITS Regions

17. ITS Regions Highly conserved region, coding region

18. ITS Regions Highly conserved region, coding region Variation, Key for diagnostics

19. COXII Regions

20. COXII Regions

21. COXII Regions Example) Phytophthora infestans Phytophthora mirabilis Phytophthora phaseoli

22. Evolution of Phytophthora B A C D E

23. More complex, evolutionary questions

24. More complex, evolutionary questions

25. More complex, evolutionary questions Using full genome sequences, Alignment, EST sequence

26. More complex, evolutionary questions Using full genome sequences, Alignment, EST sequence

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. 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. 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. DNA amplification and sequencing http://www.phytophthoradb.org

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. Result

33. Result

34. Result

35. Phytophthora Database Global Phytophthora Network Plant Pathogen Database and Genomic Initiative at Penn State University since 2005 Thank you.