The genome sequence of Atlantic cod reveals a unique immune system

Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway.
Nature (Impact Factor: 41.46). 08/2011; 477(7363):207-10. DOI: 10.1038/nature10342
Source: PubMed


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.

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    • "was used. This microarray design is partly based on the Atlantic cod gene set described in Star et al. (2011) as well as EST sequences from various cod tissues/developmental stages. Two hundred nanograms of total RNA was used to synthetize Cy3 labeled cRNA, using the Low "

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    • "In salmon eggs the most overrepresented pathways were related to immune, excretory, nervous system and signal transduction pathways (Fig. 4b). The significant differences in immune pathways represented in between cod and salmon eggs (Fig. 4b), probably coincides with what has already been observed for cod, namely that the cod is lacking a major players in the immune system including MHC II and CD4 (Star et al., 2011). Thereby, since cod lacks these major players it has been suggested that cod has an evolutionary different response to pathogens . "
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    ABSTRACT: Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if species specific "egg life history traits" can be hidden in the unfertilized egg. This was done by investigating egg transcriptome differences between Atlantic salmon and Atlantic cod. Salmon and cod eggs were selected due to their largely differencing phenotypes. An oligo microarray analysis was performed on ovulated eggs from cod (n = 8) and salmon (n = 7). The arrays were normalized to a similar spectrum for both arrays. Both arrays were re-annotated with SWISS-Prot and KEGG genes to retrieve an official gene symbol and an orthologous KEGG annotation, in salmon and cod arrays this represented 14,009 and 7,437 genes respectively. The probe linked to the highest gene expression for that particular KEGG annotation was used to compare expression between species. Differential expression was calculated for genes that had an annotation with score >300, resulting in a total of 2,457 KEGG annotations (genes) being differently expressed between the species (FD > 2). This analysis revealed that immune, signal transduction and excretory related pathways were overrepresented in salmon compared to cod. The most overrepresented pathways in cod were related to regulation of genetic information processing and metabolism. To conclude this analysis clearly point at some distinct transcriptome repertoires for cod and salmon and that these differences may explain some of the species-specific biological features for salmon and cod eggs. Mol. Reprod. Dev. 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
    Molecular Reproduction and Development 04/2015; DOI:10.1002/mrd.22487 · 2.53 Impact Factor
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    • "Taken together, our results from in vitro and in vivo studies confirm that ultrapure LPS have a stimulatory effect on inflammatory genes in cod. Initially, we believed this to be an exclusive feature of cod due to its already revealed unique organisation of its immune system [12]. However, this claim did not hold true since we also proved a stimulatory effect by ultrapure LPS in salmon. "
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