Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).

Anson Kk Wu,John S Lumsden,Janet I Macinnes,Brian Dixon,Andrew M Kropinski

doi:10.1186/1944-3277-10-3

Abstract

Flavobacterium psychrophilum is the causative agent of bacterial cold water disease and rainbow trout fry mortality syndrome in salmonid fishes and is associated with significant losses in the aquaculture industry. The virulence factors and molecular mechanisms of pathogenesis of F. psychrophilum are poorly understood. Moreover, at the present time, there are no effective vaccines and control using antimicrobial agents is problematic due to growing antimicrobial resistance and the fact that sick fish don’t eat. In the hopes of identifying vaccine and therapeutic targets, we sequenced the genome of the type strain ATCC 49418 which was isolated from the kidney of a Coho salmon (Oncorhychus kisutch) in Washington State (U.S.A.) in 1989. The genome is 2,715,909 bp with a G+C content of 32.75%. It contains 6 rRNA operons, 49 tRNA genes, and is predicted to encode 2,329 proteins.

Highlights

Flavobacterium psychrophilum is a Gram-negative pathogen that infects all species of salmonid fish and has been found to infect eel and three species of cyprinids [1,2,3]
Growth conditions and DNA isolation F. psychrophilum ATCC 49418T was originally obtained from the American Type Culture Collection [15] and was stored in a frozen glycerol stock (15%) at −70°C
The two contigs were collapsed into one and the sequence was opened in a region homologous to the Ori of F. psychrophilum JIP02/86 resulting in another two contigs

Summary

Introduction

Flavobacterium psychrophilum is a Gram-negative pathogen that infects all species of salmonid fish and has been found to infect eel and three species of cyprinids [1,2,3]. Growth conditions and DNA isolation F. psychrophilum ATCC 49418T was originally obtained from the American Type Culture Collection [15] and was stored in a frozen glycerol stock (15%) at −70°C It was grown for 4 days at 12°C on modified cytophaga agar [48] containing 0.06% (w/v) tryptone, 0.05% yeast extract, 0.02% beef extract, 0.02% sodium acetate, 0.05% anhydrous calcium chloride, 0.05% magnesium chloride, 0.05% potassium chloride, 1.5% agar, 0.02% gelatin, pH 7.5. The preassembled reads for the seeds are generated using PBDAG-Con [51] to create corrected consensus sequences in addition to quality analysis of the seeds This script uses multiple sequence alignments and a directed acyclic graph to produce the best consensus reads possible. It avoids generating chimeric sequences (sequences with artifacts) for

6.14 Function unknown

Findings

Conclusion