Project Number: 1930-32000-001-02
Project Type: Reimbursable

Start Date: Jan 01, 2004
End Date: Dec 31, 2005

Objective:
The objective of this cooperative research project is to completely sequence the genome of the fish pathogen Renibacterium salmoninarum. Automated and manual open reading frame annotation will be performed. Upon completion of this project, the annotated sequence will be deposited in the GenBank Microbial Genome database. A workshop will be co-hosted to present the findings of this project to interested parties in both the fish disease and broader scientific community. Renibacterium salmoninarum clones from the small and large insert libraries will be made available upon request.

Approach:
A random, small-insert shotgun library will be constructed from R. salmoninarum DNA by standard methods and subjected to high throughput paired-end sequencing. Approximately 62,000 inserts will be sequenced to complete an 8x coverage of the 3.4 Megabase genome. A large insert fosmid library will be constructed to correctly order contigs and to fill in the remaining gaps using a primer-walking strategy. The finished sequence will be subjected to automated open reading frame calling using CRITICA, followed by a preliminary assignment of gene names using the ERGO software suite provided by Integrated Genomics. After this stage, the computer-generated annotation of the genome will be subjected to manual annotation. The annotated genome will be transferred to the GenBank Microbial Genomes database.

Project Team

Wiens, Gregory

Related National Programs

Aquaculture (106)