The genome sequence of Atlantic cod reveals a unique immune system

By Bastiaan Star, A. Nederbragt, S. Jentoft, U. Grimholt, Martin Malmstrøm, T. Gregers, Trine B. Rounge, Jonas Paulsen, M. H. Solbakken, Animesh Sharma and 32 more. Nature, 2011

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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.

Subfields: Immunology

View Paper: https://www.semanticscholar.org/paper/00303bce57f96dadf1b5c32f924dc0ea08783e26

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Citations in the corpus

• Ensembl 2012 (2011, methodology): “The Atlantic cod (Gadus morhua) was fully annotated and released on our preview site in conjunction with the genome article (17) and will be released on the main site in late 2011 as part of Ensembl release 65.”
• The zebrafish (Danio rerio) as a model organism, with emphasis on applications for finfish aquaculture research (2014, background): “There are 255 293 public ESTs in the NCBI for Atlantic cod (Gadus morhua), and its genome was recently published (Johansen et al. 2009; Star et al. 2011) as well as it has been recently published the genome for other species, the tilapia (Guyon et al.”
• Recent advances of genome mapping and marker‐assisted selection in aquaculture (2013, background): “Atlantic cod, Gadus morhua, Gadidae and Pacific oyster Crassostrea gigas, Ostreidae) have already been published (Star et al. 2011; Zhang et al. 2012).”
• Major Histocompatibility Complex Genomics and Human Disease (2013, neutral): “Interestingly, cod appear to have lost class II functions altogether (109).”
• Egg quality in fish: Present and future challenges (2015, background): “To date, the genome sequences of only a few economically relevant fish species have been published (Star et al., 2011; Henkel et al., 2012; Berthelot et al., 2014; Brawand et al., 2014).”
• The Amborella Genome and the Evolution of Flowering Plants (2013, background): “, Genomic duplication, fractionation and the origin of regulatory novelty, Genetics 166, 935–945 (2004).”