title: The genome sequence of Atlantic cod reveals a unique immune system.
abstract: Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
authors.affiliation: Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway.
authors.forename: Bastiaan
authors.initials: B
authors.lastname: Star
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Nederbragt
authors.forename: Sissel
authors.initials: S
authors.lastname: Jentoft
authors.forename: Unni
authors.initials: U
authors.lastname: Grimholt
authors.forename: Martin
authors.initials: M
authors.lastname: Malmstrøm
authors.forename: Tone F
authors.initials: TF
authors.lastname: Gregers
authors.forename: Trine B
authors.initials: TB
authors.lastname: Rounge
authors.forename: Jonas
authors.initials: J
authors.lastname: Paulsen
authors.forename: Monica H
authors.initials: MH
authors.lastname: Solbakken
authors.forename: Animesh
authors.initials: A
authors.lastname: Sharma
authors.forename: Ola F
authors.initials: OF
authors.lastname: Wetten
authors.forename: Anders
authors.initials: A
authors.lastname: Lanzén
authors.forename: Roger
authors.initials: R
authors.lastname: Winer
authors.forename: James
authors.initials: J
authors.lastname: Knight
authors.forename: Jan-Hinnerk
authors.initials: JH
authors.lastname: Vogel
authors.forename: Bronwen
authors.initials: B
authors.lastname: Aken
authors.forename: Oivind
authors.initials: O
authors.lastname: Andersen
authors.forename: Karin
authors.initials: K
authors.lastname: Lagesen
authors.forename: Ave
authors.initials: A
authors.lastname: Tooming-Klunderud
authors.forename: Rolf B
authors.initials: RB
authors.lastname: Edvardsen
authors.forename: Kirubakaran G
authors.initials: KG
authors.lastname: Tina
authors.forename: Mari
authors.initials: M
authors.lastname: Espelund
authors.forename: Chirag
authors.initials: C
authors.lastname: Nepal
authors.forename: Christopher
authors.initials: C
authors.lastname: Previti
authors.forename: Bård Ove
authors.initials: BO
authors.lastname: Karlsen
authors.forename: Truls
authors.initials: T
authors.lastname: Moum
authors.forename: Morten
authors.initials: M
authors.lastname: Skage
authors.forename: Paul R
authors.initials: PR
authors.lastname: Berg
authors.forename: Tor
authors.initials: T
authors.lastname: Gjøen
authors.forename: Heiner
authors.initials: H
authors.lastname: Kuhl
authors.forename: Jim
authors.initials: J
authors.lastname: Thorsen
authors.forename: Ketil
authors.initials: K
authors.lastname: Malde
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Lei
authors.initials: L
authors.lastname: Du
authors.forename: Steinar D
authors.initials: SD
authors.lastname: Johansen
authors.forename: Steve
authors.initials: S
authors.lastname: Searle
authors.forename: Sigbjørn
authors.initials: S
authors.lastname: Lien
authors.forename: Frank
authors.initials: F
authors.lastname: Nilsen
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
authors.forename: Stig W
authors.initials: SW
authors.lastname: Omholt
authors.forename: Nils Chr
authors.initials: NC
authors.lastname: Stenseth
authors.forename: Kjetill S
authors.initials: KS
authors.lastname: Jakobsen
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D048389:Gadus morhua / Q000235:genetics* / Q000276:immunology*; D016678:Genome / Q000235:genetics*; D023281:Genomics; D006454:Hemoglobins / Q000235:genetics; D007107:Immune System / Q000276:immunology*; D007109:Immunity / Q000235:genetics* / Q000276:immunology; D008285:Major Histocompatibility Complex / Q000235:genetics / Q000276:immunology; D008297:Male; D011110:Polymorphism, Genetic / Q000235:genetics; D026801:Synteny / Q000235:genetics; D051193:Toll-Like Receptors / Q000235:genetics
chemical_list: D006454:Hemoglobins; D051193:Toll-Like Receptors