ALBERT

Description: 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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537168/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537168/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Star, Bastiaan -- Nederbragt, Alexander J -- Jentoft, Sissel -- Grimholt, Unni -- Malmstrom, Martin -- Gregers, Tone F -- Rounge, Trine B -- Paulsen, Jonas -- Solbakken, Monica H -- Sharma, Animesh -- Wetten, Ola F -- Lanzen, Anders -- Winer, Roger -- Knight, James -- Vogel, Jan-Hinnerk -- Aken, Bronwen -- Andersen, Oivind -- Lagesen, Karin -- Tooming-Klunderud, Ave -- Edvardsen, Rolf B -- Tina, Kirubakaran G -- Espelund, Mari -- Nepal, Chirag -- Previti, Christopher -- Karlsen, Bard Ove -- Moum, Truls -- Skage, Morten -- Berg, Paul R -- Gjoen, Tor -- Kuhl, Heiner -- Thorsen, Jim -- Malde, Ketil -- Reinhardt, Richard -- Du, Lei -- Johansen, Steinar D -- Searle, Steve -- Lien, Sigbjorn -- Nilsen, Frank -- Jonassen, Inge -- Omholt, Stig W -- Stenseth, Nils Chr -- Jakobsen, Kjetill S -- 098051/Wellcome Trust/United Kingdom -- England -- Nature. 2011 Aug 10;477(7363):207-10. doi: 10.1038/nature10342.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21832995" target="_blank"〉PubMed〈/a〉

Description: The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lien, Sigbjorn -- Koop, Ben F -- Sandve, Simen R -- Miller, Jason R -- Kent, Matthew P -- Nome, Torfinn -- Hvidsten, Torgeir R -- Leong, Jong S -- Minkley, David R -- Zimin, Aleksey -- Grammes, Fabian -- Grove, Harald -- Gjuvsland, Arne -- Walenz, Brian -- Hermansen, Russell A -- von Schalburg, Kris -- Rondeau, Eric B -- Di Genova, Alex -- Samy, Jeevan K A -- Olav Vik, Jon -- Vigeland, Magnus D -- Caler, Lis -- Grimholt, Unni -- Jentoft, Sissel -- Inge Vage, Dag -- de Jong, Pieter -- Moen, Thomas -- Baranski, Matthew -- Palti, Yniv -- Smith, Douglas R -- Yorke, James A -- Nederbragt, Alexander J -- Tooming-Klunderud, Ave -- Jakobsen, Kjetill S -- Jiang, Xuanting -- Fan, Dingding -- Hu, Yan -- Liberles, David A -- Vidal, Rodrigo -- Iturra, Patricia -- Jones, Steven J M -- Jonassen, Inge -- Maass, Alejandro -- Omholt, Stig W -- Davidson, William S -- England -- Nature. 2016 Apr 18;533(7602):200-5. doi: 10.1038/nature17164.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, As NO-1432, Norway. ; Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada. ; J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA. ; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As NO-1432 Norway. ; Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea 90187, Sweden. ; Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742-2431, USA. ; Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA. ; Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania 19122-6078, USA. ; Department of Biology, Temple University, Philadelphia, Pennsylvania 19122-6078, USA. ; Center for Mathematical Modeling, University of Chile, Santiago 8370456, Chile. ; Center for Genome Regulation, University of Chile, Santiago 8370415, Chile. ; Medical Genetics, Oslo University Hospital and University of Oslo, Oslo NO-0424, Norway. ; Department of Virology, Norwegian Veterinary Institute, Oslo NO-0454, Norway. ; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway. ; CHORI, Oakland, California 94609, USA. ; AquaGen, Trondheim NO-7462, Norway. ; Nofima, Tromso NO-9291, Norway. ; National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, West Virginia 25430, USA. ; Beckman Genomics, Danvers, Massachusetts 01923, USA. ; Courtagen Life Sciences, Woburn, Massachusetts 01801, USA. ; BGI-Shenzhen, Shenzhen 518083, China. ; Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, Santiago 9170022, Chile. ; Faculty of Medicine, University of Chile, Santiago 8380453, Chile. ; Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada. ; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada. ; Department of Informatics, University of Bergen, Bergen NO-6020, Norway. ; Centre for Biodiversity Dynamics, Department of Biology, NTNU - Norwegian University of Science and Technology, Trondheim NO-7491, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27088604" target="_blank"〉PubMed〈/a〉

Description: The IPD-MHC Database project ( http://www.ebi.ac.uk/ipd/mhc/ ) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group.