ALBERT

Description: How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod ( Gadus morhua L.) along a natural salinity gradient, ranging from 35 in the North Sea to 7 within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.

Description: The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marcussen, Thomas -- Sandve, Simen R -- Heier, Lise -- Spannagl, Manuel -- Pfeifer, Matthias -- International Wheat Genome Sequencing Consortium -- Jakobsen, Kjetill S -- Wulff, Brande B H -- Steuernagel, Burkhard -- Mayer, Klaus F X -- Olsen, Odd-Arne -- New York, N.Y. -- Science. 2014 Jul 18;345(6194):1250092. doi: 10.1126/science.1250092.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, Norwegian University of Life Sciences, 1432 As, Norway. ; Department of Plant Sciences, Norwegian University of Life Sciences, 1432 As, Norway. simen.sandve@nmbu.no. ; Stromsveien 78 B, 0663 Oslo, Norway. ; Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany. ; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway. ; The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25035499" target="_blank"〉PubMed〈/a〉

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: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

Description: Pseudochattonella farcimen (Eikrem, Edvardsen, et Throndsen) is a unicellular alga belonging to the Dictyochophyceae (Heterokonta). It forms recurring blooms in Scandinavian coastal waters, and has been associated to fish mortality. Here we report the sequencing and analysis of 10,368 expressed sequence tags (ESTs) corresponding to 8,149 unique gene models from this species. Compared to EST libraries from other heterokonts, P. farcimen contains a high number of genes with functions related to cell communication and signaling. We found several genes encoding proteins related to fatty acid metabolism, including eight fatty acid desaturases and two phospholipase A2 genes. Three desaturases are highly similar to 4-desaturases from haptophytes. P. farcimen also possesses three putative polyketide synthases (PKSs), belonging to two different families. Some of these genes may have been acquired via horizontal gene transfer by a common ancestor of brown algae and dictyochophytes, together with genes involved in mannitol metabolism, which are also present in P. farcimen. Our findings may explain the unusual fatty acid profile previously observed in P. farcimen, and are discussed from an evolutionary perspective and in relation to the ichthyotoxicity of this alga.

Description: Pseudochattonella farcimen (Eikrem, Edvardsen, et Throndsen) is an ichthyotoxic alga within the Dictyochophyceae (Heterokonta), which has been shown to form blooms in Scandinavian waters every year since 1998. To improve our understanding of the biology of this alga and to facilitate future genomic studies, we report the sequencing and analysis of 〉10,000 expressed sequence tags (ESTs) corresponding to 8149 gene models from this species. A direct comparison with EST libraries from other heterokonts revealed several functional categories to be significantly overrepresented among the P. facimen ESTs, such as genes involved in cell communication, transporters, or genes targeted to cell organelles. Interestingly, P. farcimen ESTs also code for a high proportion (1.4%) of proteins related to fatty acid metabolism, including eight fatty acid desaturases and two phospholipase A2 genes. Three of the desaturases belong to a family of delta-4 desaturases, known so far only from haptophytes, where they catalyze the conversion of n3-docosapentaenoic (n3-DPA) acid to docosahexaenoic acid (DHA). These findings may partially explain the unusual fatty acid profiles observed in P. farcimen and are discussed both from an evolutionary point of view and in relation the ichthyotoxic effects of this alga