Plant Pathology Seminar

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2009 Spring Plant Pathology Seminar

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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.
  • I’m going to talk little bit about Phytophthora and Pythium.
    I’ll continue to introduce the database issues in biology
    The main topic will be covered in Phytophthora Database part.
    Pythium DB, Future direction and acknowledgement will be followed
  • 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.
  • Well, let’s talk about the Database.
    Database is the collection of data.
    Database systems are designed to manage large bodies of information.
    When you search some book chapters or journal papers, you can simply input a keyword in the google scholar or pubmed. Because the database already constructed, this is possible.
  • Personally, my perspective on database has been changed like this.
    Phytophthora Database -> Phytophthora Database
    Sort of Geek -> Biologist and Educator
  • How can we use database in Plant Pathology?
    Well, here are some examples.
  • 2009 Database issue in Nucleic Acid Research introduced new 95 database available.
    The biology database collection, the number is 1170.
    I think actual number of biological databases will be larger than this number.
    Oxford journal also started new journal ‘Database and Curation’.
  • When you visit the Genomeonline.org
    You can also follow lots of sequence genome database.
    Wow. It’s been exponentially increased since 1995.
  • This efforts was initiated since 2006, realizing the importance why we have to keep our resources.
    It’s important issue not only for agricultural security but also plant pathology itself!
  • There are three specific objectives in this project, the first of which is to establish evolutionary relationships among Phytophthora species to help pathologists develop diagnostic tools and assess risk of newly isolated pathogen isolate.
    Second objective is to provide an informatics platform that supports the archiving, sharing, and use of available data to solve disease problems.
    To simply put it, we are trying to build a forensic database similar to the genetic fingerprint databases law enforcement agencies are using to identify criminals, but with more functionality
  • There are three specific objectives in this project, the first of which is to establish evolutionary relationships among Phytophthora species to help pathologists develop diagnostic tools and assess risk of newly isolated pathogen isolate.
    Second objective is to provide an informatics platform that supports the archiving, sharing, and use of available data to solve disease problems.
    To simply put it, we are trying to build a forensic database similar to the genetic fingerprint databases law enforcement agencies are using to identify criminals, but with more functionality
  • Dr. Alan collmer question what is difference the Phytophthora Database from Virginia Tech?
  • This outlines the organization of the Phytophthora Database. It consists of three layers.
    The basal layer contains databases of genotypes and phenotypes of pathogens.
    The middleware links data analysis and visualization tools to the UI.
    The user interface provides customized means for data storage and sharing among the users.
  • Here is one of example page for Phytophthora infestans.
    The book written by Donald C. Erwin and Olaf K. Riberiro in 1997.
    It is digitalized and stored in the Phytophthora Database.
    Each species page also provide the nomanclature database from USDA.
  • Plant Pathology Seminar

    1. 1. Phytophthora and Pythium DatabasesPhytophthora and Pythium Databases A growing cyberinfrastructure supporting the identificationA growing cyberinfrastructure supporting the identification and monitoring of major pathogen groupsand monitoring of major pathogen groups Bongsoo Park, Department of Plant Pathology The Pennsylvania State University
    2. 2. OutlineOutline  Phytophthora & Pythium  Database Issues in Biology  Phytophthora Database ◦ Letter to Phytophthora Community ◦ Current needs and Problems ◦ Specific Objectives of the PD Project ◦ Functionality of the PD ◦ How can we use this database  Pythium Database  Future Directions  Acknowledgements
    3. 3. Phytophthora & PythiumPhytophthora & Pythium  Taxonomy Eukaryota > Chromista (Kingdom)> Oomycota > Oomycetes(Class)> Peronosporales > Pythiaceae > Phytophthora Facultative parasites Soil- and water-borne
    4. 4. Phytophthora & PythiumPhytophthora & Pythium 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) Nathanael Pringsheim (1823-1894) http://www.deutsche-botanische-gesellschaft.de/ Heinrich Anton de Bary (1831-1888) http://en.wikipedia.org/wiki/Heinrich_Anton_de_Bary
    5. 5. Sudden Oak Death (SOD) in CA and OR Serious threat to the US forests Phytophthora ramorum Symptoms include bleeding cankers on the tree’s trunk and dieback of the foliage.
    6. 6. Tanoak canker Tip necrosis on Rhododendron leaves Ivors, K. http://www.phytophthoradb.org/ Ivors, K. http://www.phytophthoradb.org/
    7. 7. Database: DefinitionDatabase: Definition  Database: The collection of Data  Database systems are designed to manage large bodies of information.  Management of data involves both defining structures for stored information & providing mechanisms for the management and utilization of the information. PD
    8. 8. Change in my perspectiveChange in my perspective Phytophthora Database Phytophthora Database
    9. 9. Plant Pathology Database(?)Plant Pathology Database(?)  Pathogen Genome Sequences  Plant Pathogen or Disease Images  Host & Disease reports  Book Chapters (PD : Phytophthora Diseases Worldwide)  Experimental Protocols (http://openwetware.org)  Expertise Human Resource (http://www.apsnet.org,http://www.epernicus.com)  Communication Repository (Forum,Blog, Twitter)
    10. 10. New Journal for DatabaseNew Journal for Database  The 2009 issue of Nucleic Acid Research includes descriptions of 179 databases, of which 95 are new.  Nucleic Acids Research online Molecular Biology Database Collection (Total 1170!) (http://www.oxfordjournals.org/nar/database/a/) Welcome to Database: The Journal of Biological Databases and Curation New Journal will be initiated in 2009
    11. 11. Genome Sequencing DatabaseGenome Sequencing Database  Major Genome DBs: NCBI, EBI, DDJB  Genomes OnLine Database http://www.genomesonline.org/
    12. 12. Letter to Phytophthora CommunityLetter to Phytophthora Community Phytopathology 2006, Volume 96, Number 9, Pages 920-925
    13. 13.  Global genotypic and phenotypic diversity of plant pathogens and their distribution and dynamics need to be analyzed and archived in a format that can be easily accessed and visualized. • Difficulties in identifying and tracking pathogens • High degrees of pathogen diversity and dynamics in nature Current Needs & ProblemsCurrent Needs & Problems
    14. 14.  Global genotypic and phenotypic diversity of plant pathogens and their distribution and dynamics need to be analyzed and archived in a format that can be easily accessed and visualized. • Difficulties in identifying and tracking pathogens • High degrees of pathogen diversity and dynamics in nature • Urgent need for global cooperation in dealing with disease problems • Properly archiving data is as important as generating new data! Current Needs & ProblemsCurrent Needs & Problems
    15. 15.  Pathogen culture collections are invaluable assets • Primary links to past disease epidemics and research activities, including genomics Current Needs & ProblemsCurrent Needs & Problems
    16. 16. To establish a comprehensive phylogenetic framework for the genus Phytophthora. To build a cyberinfrastructure that archives the genotypes, phenotypes, and distribution of individual Phytophthora species/isolates and provides data analysis and visualization tools. To develop and optimize molecular diagnostic tools for detecting and identifying Phytophthora species. Specific Objectives of the PD ProjectSpecific Objectives of the PD Project
    17. 17. To establish a comprehensive phylogenetic framework for the genus Phytophthora. To build a cyberinfrastructure that archives the genotypes, phenotypes, and distribution of individual Phytophthora species/isolates and provides data analysis and visualization tools. To develop and optimize molecular diagnostic tools for detecting and identifying Phytophthora species. Specific Objectives of the PD ProjectSpecific Objectives of the PD Project
    18. 18. Development of new phylogenetic markers based on the genome sequences of P. ramorum, P. capsici, P. sojae and P. infestans. ProgressProgress
    19. 19. Development of new phylogenetic markers based on the genome sequences of P. ramorum, P. capsici, P. sojae and P. infestans. Conducted a genus-wide phylogenetic analysis using representative species/isolates. ProgressProgress
    20. 20. Development of new phylogenetic markers based on the genome sequences of P. ramorum, P. capsici, P. sojae and P. infestans. Conducted a genus-wide phylogenetic analysis using representative species/isolates. Genotypic identification of ~3,000 isolates (>90 species). Establishment of the Phytophthora Database. Characterization of individual species complexes (e.g., P. cinnamomi, P. capsici) ProgressProgress
    21. 21. Phytophthora Database The number Member 381 Country 41 Species Description 94 Pathogen Isolates 1,762 Genetic Marker Sequences 3,641 GlobalGlobal PhytophthoraPhytophthora NetworksNetworks
    22. 22. Phytophthora infestansPhytophthora infestans Genome DatabaseGenome Database
    23. 23. Phytophthora sojaePhytophthora sojae EST DatabaseEST Database Starting with Phytophthora sojae, EST sequences http://vmd.vbi.vt.edu/EST/
    24. 24. PhytophthoraPhytophthora genus, Forensic Databasegenus, Forensic Database http://www.phytophthoradb.org
    25. 25. Park et al. Plant Disease (2008) 92: 966-972 Phytophthora DatabasePhytophthora Database
    26. 26. 55 C Phytophthora infestansPhytophthora infestans Phytophthora Disease Worldwide Donald C. Erwin Olaf K. Ribeiro
    27. 27. Data Submission BLAST Search Virtual Gel Sequence Alignment Phylogenetic Tree Data Download & Storage Marker Sequence Database Cart & Folder Functionality of the PDFunctionality of the PD
    28. 28. The available programs in PDThe available programs in PD BLAST Search ClustalW Sequence Alignment Phyloviewer Virtual RFLP Cart & Folder System Ver 2.0 (Ver2.2 new) Ver 1.7 (Ver2.0 new) Ver 1.0 Ver 1.0 Ver 1.0 Basic Local Alignment Search Tool Multiple Sequence Alignment Program Phylogenetic Tree drawing Program Virtual Gel Running Program Storaging Sharing Tool Myers, E. Altschul S.F. Gish W. Miller E. W. Lipman D. J. Gibson T. Thompson J. Higgins D. Park B. Park J. Park J. Park B. Park J. Since 1990 Since 1994 Since 2007 Since 2007 Since 2006
    29. 29. How can we use the database?How can we use the database?  Database curation works  GenBank vs PD GenBank 2008 GenBank 2009 PD 2008 PD 2009
    30. 30. Datamining ofDatamining of PhytophthoraPhytophthora ITSITS  Species Apr. 20081 Jan. 20091 P. capsici 197 198 P. cactorum 164 177 P. cinnamomi 155 162 P. cryptogea 149 152 P. infestans 144 146 P. citricola 134 153 P. nicotianae 111 169 P. megasperma 92 95 P. citrophthora 83 83 P. ramorum 75 77 Phytophthora sp. 152 213 Other species 969 (90) 1,045(91) Total number 2,425 2,670 NCBI Accession # Submitted identity Likely identity AF228096 P. drechsleri P. cajani AF228093 P. drechsleri P. melonis AF228095 P. drechsleri P. melonis AY251650 P. drechsleri P. melonis AY251652 P. drechsleri P. cinnamomi AY251651 P. drechsleri P. melonis AY659656 P. cryptogea P. melonis AY745754 P. nicotianae Not sure DQ092419 P. alni Not sure AB217679 P. megasperma Not sure AB217685 P. sojae P. citricola DQ831527 P. cinnamomi P. cryptogea DQ821190 P. nicotianae P. cryptogea EF173471 P. infestans Not sure DQ501284 P.drechsleri P. melonis DQ831524 P. megasperma P. medicanis AB217680 P. megasperma Not sure EF490382 P. citricola P. pseudosyringae EU044732 P. citricola P. cactorum EU194394 P. megasperma P. cryptogea EF490383 P. pseudosyringae P. citricola EU000073 P. cryptogea P. megasperma EU194389 P. megasperma P. erythorosepica AB367382 P. drechsleri P. niederhauserii EQ490382 P. citricola P. pseudosyringae
    31. 31. How can we use the database?How can we use the database?  Quality of PD will ensure much better search results, and we will address the importance of community data curation. PD
    32. 32. How can we use the database?How can we use the database? PD  Phylogenetic tree will be updated and studied in more systemic and organized manners. Jamie E. Blair et al, Fungal Genetics & Biology
    33. 33. How can we use the database?How can we use the database?  Phylogenetic tree will be updated and studied in more systemic and organized manners. Phyloviewer program will be updated and utilized in PD. Phyloviewer program, created by B. Park. 2007
    34. 34. How can we use the databaseHow can we use the database  RFLP Virtual Gel  Cyber lab, it’s just first step. Virtual RFLP program, created by J. Park. 2007
    35. 35. How can we use the database?How can we use the database?  Presenting a standardized database schema to the global plant pathology community PD Species Information Isolate Information Sequence Information Being a standard database Intensive collaboration will be possible.
    36. 36. Pythium DatabasePythium Database http://www.pythiumdb.org
    37. 37. Future DirectionsFuture Directions  Pythium Database working with Dr. Moorman and others (http://www.pythiumdb.org)  Fusarium Database working with Dr. Geiser and others (http://isolate.fusariumdb.org)  Being the standard of Plant Pathogen Isolate Databases from Plant Saving University  Working on GIS tools with ZedX  Working on genomic browser and comparative genomics tools in collaboration with Fungal Bioinformatics Lab
    38. 38. Future DirectionsFuture Directions Big pictures for plant pathogen database PD Pythium DB Fusarium DB
    39. 39. Future DirectionsFuture Directions Integration all available tools and data from genome to geospatial context Dr. Kang’s proposal
    40. 40. AckledgementsAckledgements Penn State  Dr. Seogchan Kang  Dr. David M. Geiser  Dr. Gary W. Moorman  Dr. Michele A. Mansfield  Dr. Frederick Gildow  Dr. Maria del Mar Jimenez-Gasco  Dr. Beth K. Gugino  Dr. Yong-Hwan Lee (Seoul National University, Korea)  Dr. Jamie E. Blair (Franklin & Marchall College, PA)  Dr. Kelly Ivors (North Carolina State University, NC)  Dr. Mike Coffey (University of California in Riverside, CA)  Dr. Frank Martin (USDA-ARS)  Seogchan Kang’s Lab members in Penn State  Fungal Bioinformatics Lab members in Seoul National Univ  Department of Plant Pathology  USDA Plant Biosecurity grant (2008-55605-18773)
    41. 41. Thank you.Thank you. http://ppathblog.psu.edu
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