title: The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.
abstract: BACKGROUND
  The fish pathogen Aliivibrio salmonicida is the causative agent of cold-water vibriosis in marine aquaculture. The Gram-negative bacterium causes tissue degradation, hemolysis and sepsis in vivo.
  
  
  RESULTS
  In total, 4 286 protein coding sequences were identified, and the 4.6 Mb genome of A. salmonicida has a six partite architecture with two chromosomes and four plasmids. Sequence analysis revealed a highly fragmented genome structure caused by the insertion of an extensive number of insertion sequence (IS) elements. The IS elements can be related to important evolutionary events such as gene acquisition, gene loss and chromosomal rearrangements. New A. salmonicida functional capabilities that may have been aquired through horizontal DNA transfer include genes involved in iron-acquisition, and protein secretion and play potential roles in pathogenicity. On the other hand, the degeneration of 370 genes and consequent loss of specific functions suggest that A. salmonicida has a reduced metabolic and physiological capacity in comparison to related Vibrionaceae species.
  
  
  CONCLUSIONS
  Most prominent is the loss of several genes involved in the utilisation of the polysaccharide chitin. In particular, the disruption of three extracellular chitinases responsible for enzymatic breakdown of chitin makes A. salmonicida unable to grow on the polymer form of chitin. These, and other losses could restrict the variety of carrier organisms A. salmonicida can attach to, and associate with. Gene acquisition and gene loss may be related to the emergence of A. salmonicida as a fish pathogen.
authors.affiliation: Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø, Norway. erikh@fagmed.uit.no
authors.forename: Erik
authors.initials: E
authors.lastname: Hjerde
authors.forename: Marit Sjo
authors.initials: MS
authors.lastname: Lorentzen
authors.forename: Matthew Tg
authors.initials: MT
authors.lastname: Holden
authors.forename: Kathy
authors.initials: K
authors.lastname: Seeger
authors.forename: Steinar
authors.initials: S
authors.lastname: Paulsen
authors.forename: Nathalie
authors.initials: N
authors.lastname: Bason
authors.forename: Carol
authors.initials: C
authors.lastname: Churcher
authors.forename: David
authors.initials: D
authors.lastname: Harris
authors.forename: Halina
authors.initials: H
authors.lastname: Norbertczak
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: Suzanne
authors.initials: S
authors.lastname: Sanders
authors.forename: Scott
authors.initials: S
authors.lastname: Thurston
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Nils Peder
authors.initials: NP
authors.lastname: Willassen
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
mesh_terms: D044165:Aliivibrio salmonicida / Q000235:genetics*; D000818:Animals; D002876:Chromosomes, Bacterial / Q000235:genetics; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D005399:Fishes / Q000382:microbiology*; D016680:Genome, Bacterial; D023281:Genomics; D010957:Plasmids / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial