Using comparative genomics to predict the epidemiology and evolution of R. solanacearum plant pathogen in the UK
Lead Research Organisation:
University of York
Department Name: Biology
Abstract
Plant pathogenic bacteria cause considerable economic losses globally due to damage to crops. Bacterial wilt, caused by the soil-borne Gram-negative quarantine bacterium Ralstonia solanacearum, is one of the most important bacterial crop diseases. In the UK, R. solanacearum causes potato brown rot. Thus far, all UK outbreaks have been associated with flooding or irrigation of potato crops from contaminated river water sources where it can persist by overwintering in the roots of its secondary host plant, Woody Nightshade. It is currently known that R. solanacearum densities peak in July-September when the water temperatures are high and that the pathogenic strains driving disease outbreaks are highly related to the environmental strains isolated from upstream of the infested potato fields. While these findings suggest that environmental reservoirs play important roles in the pathogen outbreaks, it is still unclear how the R. solanacearum population has dispersed, expanded and evolved since the first disease outbreak in 1992.
This project will use population genomics and a collection of time sampled pathogen isolates to understand the epidemiology, dispersal and evolution of R. solanacearum in the UK river system. The studentship will address three research questions:
1) Dispersal: comparison of UK isolates with an existing sequence database of R. solanacearum genomes to determine whether the UK population is genetically unique and locally adapted and to estimate the frequency of international dispersal.
2) Virulence: do the environmental isolates differ from the pathogenic isolates collected during disease outbreaks? Are some specific virulence genes more often associated with pathogenic compared to environmental isolates?
3) Evolutionary dynamics: to what extent has R. solanacearum changed during the UK disease outbreaks since 1992? Can we identify quantitative traits that are important for pathogenic vs. environmental isolates by using genome-wide association approaches (GWAS)?
The obtained results will be used to develop a genomic database that will help in identifying novel outbreak strains, to infer the likely geographic source of their origin and to match specific control management strategies against the given outbreak strain.
The project combines laboratory-based direct experimentation, next-generation genome sequencing, bioinformatics and evolutionary biology to understand the dynamics of concurrent plant pathogen outbreaks. You will also have an opportunity to develop skills in microbiology, experimental evolution, microbial ecology and hypothesis-led experimental design. As this is an interdisciplinary project, ideal candidates will have a background in or a demonstrated interest in at least one of the main subject areas - e.g. microbiology, genetics, bioinformatics, pathogenesis - and be willing to develop skills in the other areas.
This project will use population genomics and a collection of time sampled pathogen isolates to understand the epidemiology, dispersal and evolution of R. solanacearum in the UK river system. The studentship will address three research questions:
1) Dispersal: comparison of UK isolates with an existing sequence database of R. solanacearum genomes to determine whether the UK population is genetically unique and locally adapted and to estimate the frequency of international dispersal.
2) Virulence: do the environmental isolates differ from the pathogenic isolates collected during disease outbreaks? Are some specific virulence genes more often associated with pathogenic compared to environmental isolates?
3) Evolutionary dynamics: to what extent has R. solanacearum changed during the UK disease outbreaks since 1992? Can we identify quantitative traits that are important for pathogenic vs. environmental isolates by using genome-wide association approaches (GWAS)?
The obtained results will be used to develop a genomic database that will help in identifying novel outbreak strains, to infer the likely geographic source of their origin and to match specific control management strategies against the given outbreak strain.
The project combines laboratory-based direct experimentation, next-generation genome sequencing, bioinformatics and evolutionary biology to understand the dynamics of concurrent plant pathogen outbreaks. You will also have an opportunity to develop skills in microbiology, experimental evolution, microbial ecology and hypothesis-led experimental design. As this is an interdisciplinary project, ideal candidates will have a background in or a demonstrated interest in at least one of the main subject areas - e.g. microbiology, genetics, bioinformatics, pathogenesis - and be willing to develop skills in the other areas.
