The research team has studied the pathogen for nearly five years. In 2007, with resources from the Virginia Bioinformatics Institute and the Fralin Life Science Institute, Vinatzer sequenced the genome of Pseudomonas syringae pv. tomato using a Roche GS-FLX sequencer at the Virginia Bioinformatics Institute.
In 2008, Vinatzer received a $1 million, five-year Faculty Early Career Development (CAREER) Award from the National Science Foundation to continue investigation of the pathogen. Shortly thereafter, he brought Setubal, a former Virginia Tech faculty member who recently went to work for the University of Sao Paulo in Brazil, and Leman, onto the project to handle the bioinformatics and statistical aspects of the research, respectively.
First, the scientists needed to map changes in the bacterial pathogen over large spans of time. They compared DNA sequences of bacteria isolated in multiple years, dating back to 1960 and stored since then in international culture collections. Setubal, along with Nalvo Almeida, an associate professor at the Federal University of Mato Grosso do Sul, provided automated genome annotation and helped Vinatzer with identification and analysis of mutations that distinguished the sequenced genomes.
"One of the questions we asked was, did the bacteria isolated in 2000 directly evolve from the bacteria isolated in 1975, or did they evolve independently from an ancestor that lived further back in time, maybe 100 to 200 years ago?" said Vinatzer.
To answer this question, Leman, Vinatzer, and Rongman Cai of Lixian, China, a Ph.D. student in plant pathology, physiology, and weed science at Virginia Tech, used statistical methods to correlate the differences in the DNA sequences between the isolated bacteria with the years in which they were isolated to determine if the bacteria progressively became more different from the first b
|Contact: Lindsay Key|