Progress 01/01/04 to 12/31/06
Outputs
The S. scabies genome is 10.14 Mb, making it the largest Streptomyces genome to be sequenced, thus far, and among the very largest of bacterial genomes. Terminal inverted repeats on the linear chromosome are relatively short, which is surprising given the size of the genome. Bioinformatic characterization indicates that the genome has more than 9,000 genes. The pathogenicity island has undergone rearrangements in the genome, relative to S. turgidiscabies, and is no longer mobile. Those portions of the PAI for which we have markers are located in the arms of the linear chromosome, as predicted by the core genome hypothesis. Insertion of the PAI occurred in the bacA gene, as expected based on experimental data from mating studies with other species. However, one or more recombination events occurred subsequently, resulting in separation of the pathogenicity island into two or more fragments. There are 11 transposon families represented in the genome and more than 90
individual transoposons, some of which are expected to be active. We have identified many horizontally transferred regions, including new putative virulence factors, through our analysis of the genome sequence. Most of the genome is now annotated and it is possible to target regions for further genetic analysis. Our ability to conduct functional analysis is greatly facilitated by the availability of the genome and its preliminary annotation, and this work is ongoing.
Impacts
The sequence data are being used by researchers who have not previously worked with plant pathogenic Streptomyces. The Streptomyces community world-wide has focused on nonpathogenic streptomycetes, but is now embracing the S. scabies system. The genomic sequence can be used in comparative genomic analysis of Streptomyces genome strutcture, allowing researchers to understand how pathogenicity evolves in bacterial species. As this genus is the source of both clinically important antibiotics, and epidemiologically important antibiotic resistance genes, an understanding of genome evolution and the role of horizontal gene transfer in acquisition of new phenotypes will contribute greatly to our ability to control diseases and management of antibiotic resistance.
Publications
- Loria, R., J. Kers, and M. Joshi. 2006. Evolution of Plant Pathogenicity in Streptomyces. Annu. Rev. Phytopathol., 44:469-87.
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Progress 01/01/05 to 12/31/05
Outputs
Streptomyces scabies is the source of a large, mobilizable pathogenicity island (PAI). Transfer of the PAI from S. scabies to other Streptomyces species appears to have resulted in the emergence of new pathogenic species in agricultural systems. This is the first PAI to be discovered in a Gram-positive plant pathogen and, at greater than 600 kb, the largest PAI to be described in any microbe. Since the PAI is mobilizable, we will be able to investigate the evolution of pathogenicity in Streptomyces. This project will provide knowledge about the novel pathogenicity mechanisms employed by Gram-positive plant pathogens, as well as virulence factors shared with other bacteria and with fungal pathogens. The genomic sequence was generated by a whole-genome shotgun strategy. The assembled data is available for searching on the Sanger Institute blast server (http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_scabies), or for download from their FTP site
(ftp://ftp.sanger.ac.uk/pub/pathogens/ssc/). The genome is now finished. The chromosome is 10,148,695 bp with a G+C content of 71.45 percent. A preliminary gene prediction, with systematic gene identifiers, will be made available from the Sanger website soon. The S. scabies genome is the largest Streptomyces genomes to be sequenced thus far. Terminal inverted repeats are relatively short. Preliminary estimates indicate that the genome has approximately more than 9,000 genes.
Impacts
The sequence data already are being used by researchers who have not previously worked with plant pathogenic Streptomyces. The Streptomyces community world-wide has focused on nonpathogenic streptomycetes, but is now embracing the S. scabies system.
Publications
- No publications reported this period
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Progress 01/01/04 to 12/31/04
Outputs
The genomic sequence was generated by a whole-genome shotgun strategy, generating 8-10 fold genome coverage from several genomic libraries. Sequencing reads were produced using Big-dye terminators on ABI3700 and ABI3730 capillary machines, allowing long, accurate reads and trustworthy read-pairs from pUC clones. End-sequences were obtained from the large insert BAC, plasmid and lambda libraries (greater than 3-fold clone coverage of each), thus producing a scaffold to assemble the sequence contigs produced by the assembly. As the S. scabies sequence has a high G+C content, we are supplementing the pUC shotgun with a proportion of reads from shotgun clones in from M13 single-stranded vectors. Our previous experience has shown that these vectors clone high-G+C DNA better than pUC vectors, leading to less bias in the shotgun coverage. Assembly releases are being made on a biweekly basis, as finishing proceeds. The assembled data is available for searching on the Sanger
Institute blast server (http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_scabies), or for download from their FTP site (ftp://ftp.sanger.ac.uk/pub/pathogens/ssc/).
Impacts
The sequence data are being used by labs who have not previously worked with plant pathogenic Streptomyces. We have received about 10 requests for the sequenced strain from scientists who are interested in initiating studies on pathogenicity or other phenotypes in this organism. Additional research activities will accelerate the development of novel disease control strategies.
Publications
- No publications reported this period
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