title: Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.
abstract: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mock
authors.affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Otillar
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
authors.forename: Jan
authors.initials: J
authors.lastname: Strauss
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: McMullan
authors.affiliation: Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Pirita
authors.initials: P
authors.lastname: Paajanen
authors.affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.|HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.affiliation: Biology and Evolution of Marine Organisms, Computational Genomics, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
authors.forename: Remo
authors.initials: R
authors.lastname: Sanges
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Toseland
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.|Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Ward
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037, USA.|Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- and Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany.|Hochschule Bremerhaven, An der Karlsburg 8, 27568 Bremerhaven, Germany.
authors.forename: Stephan
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authors.lastname: Frickenhaus
authors.affiliation: URGI, INRA, Université Paris-Saclay, 78026 Versailles, France.
authors.forename: Florian
authors.initials: F
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authors.affiliation: Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France.
authors.forename: Alaguraj
authors.initials: A
authors.lastname: Veluchamy
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
authors.forename: Taoyang
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authors.lastname: Wu
authors.affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: Kerrie W
authors.initials: KW
authors.lastname: Barry
authors.affiliation: Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative UMR 7238, 75006 Paris, France.
authors.forename: Angela
authors.initials: A
authors.lastname: Falciatore
authors.affiliation: Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
authors.forename: Maria I
authors.initials: MI
authors.lastname: Ferrante
authors.affiliation: Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative UMR 7238, 75006 Paris, France.
authors.forename: Antonio E
authors.initials: AE
authors.lastname: Fortunato
authors.affiliation: Institute for Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Straße, 52 D-50931 Köln, Germany.|Leibniz Institute of Freshwater, Ecology and Inland Fisheries, IGB, Müggelseedamm 301, D-12587 Berlin, Germany.
authors.forename: Gernot
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authors.lastname: Glöckner
authors.affiliation: Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany.
authors.forename: Ansgar
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authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
authors.forename: Rachel
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authors.affiliation: Division of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Janech
authors.affiliation: Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Kroth
authors.affiliation: University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research Universitaetsstrasse 5, 45141 Essen, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Leese
authors.affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
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authors.initials: EA
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authors.affiliation: Marine Biomedicine and Environmental Sciences Center, Medical University of South Carolina, Charleston, South Carolina 29412, USA.
authors.forename: Barbara R
authors.initials: BR
authors.lastname: Lyon
authors.affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
authors.forename: Joel
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authors.lastname: Martin
authors.affiliation: Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany.
authors.forename: Christoph
authors.initials: C
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authors.affiliation: School of Oceanography, Center for Environmental Genomics, University of Washington, Box 357940, Seattle, Washington 98195, USA.
authors.forename: Micaela
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authors.affiliation: URGI, INRA, Université Paris-Saclay, 78026 Versailles, France.
authors.forename: Hadi
authors.initials: H
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authors.affiliation: School of Life Sciences, University of Nevada, Las Vegas, Nevada 89154, USA.
authors.forename: James A
authors.initials: JA
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authors.affiliation: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- and Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany.
authors.forename: Christiane
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authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037, USA.
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authors.initials: RE
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authors.affiliation: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- and Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany.
authors.forename: Klaus U
authors.initials: KU
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authors.affiliation: Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA.
authors.forename: Alexandra Z
authors.initials: AZ
authors.lastname: Worden
authors.affiliation: School of Oceanography, Center for Environmental Genomics, University of Washington, Box 357940, Seattle, Washington 98195, USA.
authors.forename: E Virginia
authors.initials: EV
authors.lastname: Armbrust
authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.|Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Clark
authors.affiliation: Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France.
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
authors.affiliation: Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Beverley R
authors.initials: BR
authors.lastname: Green
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
authors.forename: Vincent
authors.initials: V
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authors.affiliation: School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
authors.forename: Cock
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authors.lastname: van Oosterhout
authors.affiliation: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.|Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Igor V
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mesh_terms: D000064:Acclimatization / Q000235:genetics*; D000483:Alleles; D002245:Carbon Dioxide / Q000378:metabolism; D003080:Cold Temperature; D003624:Darkness; D017377:Diatoms / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D005615:Freezing; D020869:Gene Expression Profiling; D040961:Genetic Drift; D016678:Genome / Q000235:genetics*; D023281:Genomics; D046448:Ice Cover; D007501:Iron / Q000378:metabolism; D059645:Mutation Rate; D009792:Oceans and Seas; D010802:Phylogeny; D011995:Recombination, Genetic; D059467:Transcriptome / Q000235:genetics
chemical_list: D002245:Carbon Dioxide; D007501:Iron