Progress 01/01/04 to 12/31/05
Outputs
Progress Report 4d Progress report. This report serves to document research conducted under a Reimbursable Agreement between the ARS and the Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA. Additional details of research can be found in the report for the parent CRIS 1930-3200-002- 00D Host, Pathogen and Environmental Interactions in Cool and Cold Water Aquaculture. The project title is Genome sequencing of the vertically- transmitted fish pathogen Renibacterium salmoninarum. The following progress was made during the reporting period. The genome was closed in October 2005 by the University of Washington Genome Center. 9 X sequence coverage was obtained from small-insert library sequencing and the genome assembled using PHRED/PHRAP/CONSED software tools. The genome was closed by four rounds of AUTOFINISH followed by manual assembly. A total of 52, 686 sequence reads were incorporated in the final assembly and the gross
assembly was validated by pulsed-field gel electrophoresis. The genome of R. salmoninarum is a single, circular chromosome of 3,155,250 base pairs with 56.27% G+C content. A total of 3667 open reading frames were identified by Integrated Genomics ORF-Calling software. Using the program PSORTb v2.0, ORFs were classified as putative cytoplasmic (n=1626) , cytoplasmic membrane (n=625), cell wall (n=16), extracellular (n=132), or unknown localization (n=1268). We have combined these data with additional motif searches and immunogenicity profiles to develop a list of potential vaccine candidates for further examination. Additionally, trout immune gene expression in response to R. salmoninarum ATCC 33209 infection was measured. A workshop titled Bacterial Kidney Disease: Challenges for the 21st Century, sponsored in part by project funds and organized by the PIs, was held in Seattle WA November 15-17, 2005. At this international workshop (http://www.nwfsc.noaa.gov/bkd-conference), one
day was devoted to the announcement of first findings obtained through the R. salmoninarum Genome Project. Knowledge of the R. salmoninarum genome will serve as a foundation for identification of virulence factors, vaccine gene candidates and improved diagnostic tests. In addition, the completed R. salmoninarum genome sequence will be a template for comparison with clinical and environmental isolates.
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Progress 10/01/04 to 09/30/05
Outputs
4d Progress report. This report serves to document research conducted under a reimbursable agreement between ARS and the Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA. Additional details of research can be found in the report for the parent CRIS 1930-32000-002- 00D Host, Pathogen and Environmental Interactions in Cool and Cold Water Aquaculture. Project progress includes completion of shotgun sequencing, automated gene identification and annotation.
Impacts
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Progress 10/01/03 to 09/30/04
Outputs
4. What were the most significant accomplishments this past year? D. Progress Report: This report serves to document research conducted under a reimbursable agreement between ARS and the Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA. Additional details of research can be found in the report for the parent project 1930-32000- 001-00D, Host, Pathogen, and Environmental Interactions in Cool and Cold Water Aquaculture. Project progress includes extraction of genomic DNA for library preparation and the establishment of a project web-site (http://micro. nwfsc.noaa.gov/rs-genome/).
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