Within the Plant Pathogens programme at SCRI we analyse directly the genomes of oomycete species, Pectobacterium atrosepticum (Pba) and other bacteria, and their host plants. We are most interested in regulatory networks and interactions, secreted proteins and pathogenicity islands, and undertaking comparisons between genome sequences (Bell et al., 2004; Armstrong et al., 2005; Toth et al., 2006).

We have onsite access to an 84-node Linux cluster for large-scale comparative analyses. We also build and use custom software, and databases for the pathogens under study and their hosts, for the integration of genomic information with the results of gene knockout and high-throughput studies. At SCRI we are uniquely positioned to follow the application of results from our bioinformatics and systems analyses from hypothesis generation through plant growth and pathogen challenge, and back round to informing the next set of hypotheses.

In the Plant Pathogens programme we have developed the GenomeDiagram package (Pritchard et al., 2006), which permits the simultaneous visualisation of relationships between hundreds of genome sequences. This package has inspired a collaboration with the artist Professor Elaine Shemilt at Duncan of Jordanstone College of Art and Design, and the resulting artwork (prints, animations, and music) has been exhibited internationally.

References

Armstrong, M.R., Whisson, S.C., Pritchard, L. 102, 7766-7771. , Bos, J.I.B., Venter, E., Avrova, A.O., Rehmany, A.P., Böhme, U., Brooks, K., Cherevach, I., Hamlin, N., White, B., Fraser, A., Lord, A., Quail, M.A., Churcher, C.,  Hall, N., Berriman, M., Huang, S., Kamoun, S., Beynon, J.L. and Birch, P.R.J. 2005. An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm . Proc. Natl. Acad. Sci.USA

Bell K. S., M. Sebaihia, L. Pritchard, M. Holden, L.J. Hyman, M. C. Holeva, N. R. Thomson, S. D. Bentley, L. J. C. Churcher, K. Mungall, R. Atkin, N. Bason, K. Brooks, T. Chillingworth, K. Clark, J. Doggett, A. Fraser, Z. Hance, H. Hauser, K. Jagels, S. Moule, H. Norbertczak, D. Ormond, C. Price, M. A. Quail, M. Sanders, D. Walker, S. Whitehead, G. P. C. Salmond, P. R. J. Birch, J. Parkhill & I. K. Toth. 2004. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterisation of novel virulence factors. Proc. Natl. Acad. Sci.USA 101, 11105-11110.  

Pritchard, L., White, J.A., Birch, P.R.J., Toth, I.K. 2006. GenomeDiagram: A Python Package for the Visualisation of Large-Scale Genomic Data. Bioinformatics 22, 616-617.  

Toth IK, Pritchard L and Birch PRJ. 2006. Comparative genomics reveals what makes an enterobacterial plant pathogen. Annu. Rev. Phytopathol. 44, 305-336.