Management, analysis, and dissemination of data and resources related to the genome sequences of plant pathogenic bacteria in the species Liberibacter asiaticus and Pseudomonas syringae
CALS Impact Project
Genome resources for P. syringae and Liberibacter asiaticus are communicated through the respective websites to researchers around the world, and the site is listed by outside databases and analytic sites as the primary reference for P. syringae genome resources.
In 2009 the PPI site received more than 94,000 visits by 53,200 unique visitors. More than 460 annotation updates to the P. syringae genomes have been submitted through the site since initial sequence deposition. More than 50 new Gene Ontology terms related to virulence determinants among bacterial plant pathogens were proposed in conjunction with the PAMGO consortium and accepted by the Gene Ontology Consortium. Using these terms, more than 550 annotations have been generated for virulence factors in Pto DC3000 and are now posted on the PPI website.
Systematic comparison of the three sequenced P. syringae genomes has led to identification of: (1) highly variable regions that shed light on mechanisms of virulence evolution and (2) genes of limited distribution, representing a valuable reservoir of markers for diagnostic identification of P. syringae strains. Ongoing activities related to both websites were communicated to an international scientific community at both national and international meetings.
impact statement issue
Genome-scale sequencing of plant pathogens is an increasingly important tool for exploring host-pathogen interactions. But without systematic approaches for communicating data to the wider research community and updating genome sequence annotation, the value of these projects is severely limited.
Web-based resources for the P. syringae and Liberibacter asiaticus genome projects are developed and maintained to efficiently communicate data, tools, and other resources to a diverse community including microbiologists and plant pathologists interested in disease control. Resources in need of ongoing maintenance include guides to sequence and annotation, a portal for communicating annotation updates including Gene Ontology annotation, a guide to the nomenclature of high-interest virulence proteins included in these genomes, a means of graphically viewing the genome data, and links to other web-based resources relevant to these pathogens.
Annotation updates communicated in person, identified through literature review, and identified through research collaborations need to be efficiently transmitted to relevant outside databases and documented for easy reference by website users. Availability of a high-quality reference genomes for these bacterial species will significantly enhance the annotation quality of additional members of these bacterial species currently being sequenced.
Finally, a commitment has been made to develop and maintain lab modules and accompanying web-based resources for use by high school science classes.
impact statement response
The Pseudomonas-Plant Interaction (PPI) website (http://pseudomonas-syringae.org) and Citrus Greening/HLB Genome Resources website (http://www.citrusgreening.org/) communicate genome data and relevant analyses to the larger community for relevant plant pathogens. Both websites are continually updated to address the evolving needs of the respective research communities and leverage various resources including links, tutorials, input files for genome viewing, and guides for virulence protein nomenclature.
The PPI site is the official portal for communication of annotation updates by the research community, and updates forwarded to Genbank are documented there. Ongoing, systematic re-analysis of the Pst DC3000 genome annotation in light of proteomics data, transcript analysis, and sequence comparison are leading to a high-quality reference annotation for this species that will greatly enhance the quality of future annotations for other members of this species.
Gene Ontology terms have also been developed to capture aspects of the plant host-microbe interaction and are being used to annotate key virulence-related gene products. Also maintained on the site are the web-based components of teaching modules for high school biology students, developed in collaboration with the Cornell Institute for Biology Teachers.
The website and its associated resources have also been promoted at international conferences for plant pathologists and P. syringae researchers. In the case of the Citrus Greening website, the site also provides a password protected venue for deposition of unpublished sequence data so that the research community can benefit from access to preliminary data.
impact statement summary
The focus of my activities is the analysis, organization, and web-based dissemination of genome data for bacterial plant pathogens in the species Pseudomonas syringae and Liberibacter asiaticus.
