Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Handle URI:
http://hdl.handle.net/10754/622831
Title:
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus
Authors:
Mock, Thomas; Otillar, Robert P.; Strauss, Jan; McMullan, Mark; Paajanen, Pirita; Schmutz, Jeremy; Salamov, Asaf; Sanges, Remo; Toseland, Andrew; Ward, Ben J.; Allen, Andrew E.; Dupont, Christopher L.; Frickenhaus, Stephan; Maumus, Florian; Veluchamy, Alaguraj; Wu, Taoyang; Barry, Kerrie W.; Falciatore, Angela; Ferrante, Maria I.; Fortunato, Antonio E.; Glöckner, Gernot; Gruber, Ansgar; Hipkin, Rachel; Janech, Michael G.; Kroth, Peter G.; Leese, Florian; Lindquist, Erika A.; Lyon, Barbara R.; Martin, Joel; Mayer, Christoph; Parker, Micaela; Quesneville, Hadi; Raymond, James A.; Uhlig, Christiane; Valas, Ruben E.; Valentin, Klaus U.; Worden, Alexandra Z.; Armbrust, E. Virginia; Clark, Matthew D.; Bowler, Chris; Green, Beverley R.; Moulton, Vincent; Oosterhout, Cock van; Grigoriev, Igor V.
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, et al. (2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541: 536–540. Available: http://dx.doi.org/10.1038/nature20803.
Publisher:
Springer Nature
Journal:
Nature
Issue Date:
17-Jan-2017
DOI:
10.1038/nature20803
Type:
Article
ISSN:
0028-0836; 1476-4687
Sponsors:
We thank A. Stecher and K. Schmidt for extracting and providing environmental DNA samples and the Natural Environment Research Council UK (NERC) Biomolecular Analysis Facility (NBAF) for conducting transcriptome sequencing and providing bioinformatics support. C.B. acknowledges funding from the ERC Advanced Grant ERC-2011-ADG (Diatomite). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. PacBio sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/J010375/1) at the Earlham Institute (formerly The Genome Analysis Centre, Norwich), by members of the Platforms and Pipelines Group, PacBio assembly and sequence analysis was strategically funded by the BBSRC, Institute Strategic Programme Grant (BB/J004669/1). Additional funding for this work was provided by NERC under grants NE/I001751/1, NE/K004530/1, MGF (NBAF) grant 197, The Royal Society grant RG090774 and the Earth & Life Systems Alliance in Norwich.
Additional Links:
http://www.nature.com/nature/journal/v541/n7638/full/nature20803.html
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMock, Thomasen
dc.contributor.authorOtillar, Robert P.en
dc.contributor.authorStrauss, Janen
dc.contributor.authorMcMullan, Marken
dc.contributor.authorPaajanen, Piritaen
dc.contributor.authorSchmutz, Jeremyen
dc.contributor.authorSalamov, Asafen
dc.contributor.authorSanges, Remoen
dc.contributor.authorToseland, Andrewen
dc.contributor.authorWard, Ben J.en
dc.contributor.authorAllen, Andrew E.en
dc.contributor.authorDupont, Christopher L.en
dc.contributor.authorFrickenhaus, Stephanen
dc.contributor.authorMaumus, Florianen
dc.contributor.authorVeluchamy, Alagurajen
dc.contributor.authorWu, Taoyangen
dc.contributor.authorBarry, Kerrie W.en
dc.contributor.authorFalciatore, Angelaen
dc.contributor.authorFerrante, Maria I.en
dc.contributor.authorFortunato, Antonio E.en
dc.contributor.authorGlöckner, Gernoten
dc.contributor.authorGruber, Ansgaren
dc.contributor.authorHipkin, Rachelen
dc.contributor.authorJanech, Michael G.en
dc.contributor.authorKroth, Peter G.en
dc.contributor.authorLeese, Florianen
dc.contributor.authorLindquist, Erika A.en
dc.contributor.authorLyon, Barbara R.en
dc.contributor.authorMartin, Joelen
dc.contributor.authorMayer, Christophen
dc.contributor.authorParker, Micaelaen
dc.contributor.authorQuesneville, Hadien
dc.contributor.authorRaymond, James A.en
dc.contributor.authorUhlig, Christianeen
dc.contributor.authorValas, Ruben E.en
dc.contributor.authorValentin, Klaus U.en
dc.contributor.authorWorden, Alexandra Z.en
dc.contributor.authorArmbrust, E. Virginiaen
dc.contributor.authorClark, Matthew D.en
dc.contributor.authorBowler, Chrisen
dc.contributor.authorGreen, Beverley R.en
dc.contributor.authorMoulton, Vincenten
dc.contributor.authorOosterhout, Cock vanen
dc.contributor.authorGrigoriev, Igor V.en
dc.date.accessioned2017-02-05T13:53:44Z-
dc.date.available2017-02-05T13:53:44Z-
dc.date.issued2017-01-17en
dc.identifier.citationMock T, Otillar RP, Strauss J, McMullan M, Paajanen P, et al. (2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541: 536–540. Available: http://dx.doi.org/10.1038/nature20803.en
dc.identifier.issn0028-0836en
dc.identifier.issn1476-4687en
dc.identifier.doi10.1038/nature20803en
dc.identifier.urihttp://hdl.handle.net/10754/622831-
dc.description.abstractThe 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.en
dc.description.sponsorshipWe thank A. Stecher and K. Schmidt for extracting and providing environmental DNA samples and the Natural Environment Research Council UK (NERC) Biomolecular Analysis Facility (NBAF) for conducting transcriptome sequencing and providing bioinformatics support. C.B. acknowledges funding from the ERC Advanced Grant ERC-2011-ADG (Diatomite). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. PacBio sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/J010375/1) at the Earlham Institute (formerly The Genome Analysis Centre, Norwich), by members of the Platforms and Pipelines Group, PacBio assembly and sequence analysis was strategically funded by the BBSRC, Institute Strategic Programme Grant (BB/J004669/1). Additional funding for this work was provided by NERC under grants NE/I001751/1, NE/K004530/1, MGF (NBAF) grant 197, The Royal Society grant RG090774 and the Earth & Life Systems Alliance in Norwich.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.nature.com/nature/journal/v541/n7638/full/nature20803.htmlen
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleEvolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrusen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalNatureen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionSchool of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.en
dc.contributor.institutionDepartment of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.en
dc.contributor.institutionEuropean Molecular Biology Laboratory (EMBL) Hamburg, c/o German Electron Synchrotron (DESY), Notkestraβe 85, 22607 Hamburg, Germanyen
dc.contributor.institutionEarlham Institute, Norwich Research Park, Norwich NR4 7UH, UK.en
dc.contributor.institutionDepartment of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdomen
dc.contributor.institutionHudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.en
dc.contributor.institutionBiology and Evolution of Marine Organisms, Computational Genomics, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.en
dc.contributor.institutionSchool of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.en
dc.contributor.institutionIntegrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037, USA.en
dc.contributor.institutionMicrobial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037, USA.en
dc.contributor.institutionHochschule Bremerhaven, An der Karlsburg 8, 27568 Bremerhaven, Germany.en
dc.contributor.institutionURGI, INRA, Université Paris-Saclay, 78026 Versailles, France.en
dc.contributor.institutionEcole 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.en
dc.contributor.institutionSorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative UMR 7238, 75006 Paris, France.en
dc.contributor.institutionIntegrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.en
dc.contributor.institutionLeibniz Institute of Freshwater, Ecology and Inland Fisheries, IGB, Müggelseedamm 301, D-12587 Berlin, Germany.en
dc.contributor.institutionFachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany.en
dc.contributor.institutionDivision of Nephrology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, USA.en
dc.contributor.institutionUniversity of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research Universitaetsstrasse 5, 45141 Essen, Germany.en
dc.contributor.institutionMarine Biomedicine and Environmental Sciences Center, Medical University of South Carolina, Charleston, South Carolina 29412, USA.en
dc.contributor.institutionCoastal Studies Center, Bowdoin College, Brunswick, Maine 04011, USAen
dc.contributor.institutionZoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany.en
dc.contributor.institutionSchool of Oceanography, Center for Environmental Genomics, University of Washington, Box 357940, Seattle, Washington 98195, USA.en
dc.contributor.institutionSchool of Life Sciences, University of Nevada, Las Vegas, Nevada 89154, USA.en
dc.contributor.institutionAlfred-Wegener-Institut Helmholtz-Zentrum für Polar- and Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany.en
dc.contributor.institutionGraduate School of Oceanography, University of Rhode Island, 215 South Ferry Road, Narragansett, Rhode Island 02882-1197, USAen
dc.contributor.institutionMonterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, California 95039, USA.en
dc.contributor.institutionDepartment of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada.en
dc.contributor.institutionDepartment of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.en
kaust.authorVeluchamy, Alagurajen
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