Collaborations
USDA/ARS Plant-Microbe Interaction Research Unit
Our collaboration with ARS computational biologists Samuel Cartinhour and David Schneider began with the DC3000 genome project, which was funded in 2000 by the NSF Plant Genome Research Program. The Institute for Genome Research (TIGR), led by Robin Buell, sequenced DC3000 to completion and handled general annotation of the genome, while the ARS group developed bioinformatic methods to comprehensively identify effector gene candidates and we and other project participants experimentally validated the candidates. The strong interaction between computational and experimental biologists in our respective laboratories continues with the ARS group aimed at modeling regulatory networks controlling iron metabolism and virulence in DC3000 and our lab focused on the delivery and function of type III effectors. A shared objective of our groups is development of a systems biology approach to Pseudomonas-plant interactions.
Magdalen Lindeberg and the Pseudomonas-Plant Interaction (PPI) web-based genome resources
Magdalen Lindeberg is developing resources for researchers around the world pursuing genome-enabled studies of the three sequenced genomes of P. syringae: pv. tomato DC3000 (TIGR), pv. phaseolicola 1448A (TIGR), and pv. syringae B728a (DOE-JGI). These resources are deployed thorough the PPI website http://pseudomonas-syringae.org and are intended to foster a systems-level understanding of Pseudomonas-plant interactions by helping the community generate controlled vocabularies (particularly through Gene Ontology annotation), manage large datasets, visualize patterns in genomic data, and efficiently access annotation updates through frequent depositions with GenBank and other international databases. Our lab, with its experimental focus on the delivery and function of DC3000 type III effectors, functions as a consultant and test client for the development of PPI resources.
Gregory Martin of the Boyce Thompson Institute for Plant Research and the Department of Plant Pathology
The Martin and Collmer labs are collaborating on an NSF Plant Genome Research Program project aimed at identifying novel sources of resistance to Pseudomonas syringae in tomato. The project is aimed particularly at basal innate immunity and proposes to identify loci underlying such defenses through the use of tomato introgression lines with natural variations in resistance, advanced phenotypic analyses of plant-bacterium interactions, and pathogen mutants lacking subsets of virulence factors (which can unmask phenotypes for underlying resistance loci).
Molecular Plant-Microbe Interactions cover, November 2006.