Flavobacterium branchiophilum

The Infection and Immunity of Fish Team from the INRA in Jouy-en-Josas (France) has been studying pathogenic bacteria from the Flavobacterium genus since the first strains appeared in Europe in the 1960s. Their work has notably led to the complete revision of the genus (Bernardet, J-F, & Bowman), and the description of the Flavobacteriaceae family (Bernardet J-F, & Nakagawa,Y). They have developed methods for molecular typing, and standardized culture techniques and methods of experimental infection of the rainbow trout.

Genoscope is undertaking the sequencing of the complete genome of the bacterium, Flavobacterium branchiophilum, the pathogen responsible for gill disease, which primarily affects the salmonides.

The size of the genome of F. branchiophilum is estimated at 2.8 Mb. The genome will be sequenced by the shotgun method using two plasmid libraries with inserts of 5 kb and 10 kb, cloned respectively in multicopy plasmid pcdna2.1 and low copy number plasmid pCNS, and a fosmid library (40 kb inserts in pCC1Fos).

The sequencing of both ends of about 18,500 clones from the small insert plasmid library, 6,000 clones from the large insert plasmid library and 3,000 clones from the fosmid library should constitute a volume of 55,000 reads, corresponding to 12 genome equivalents.

The shotgun phase will be followed by an assembly step, and finishing of the sequence according to quality assurance criteria in effect at Genoscope.

Contacts: Valérie Barbe (Genoscope) - Eric Duchaud (INRA)