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Title: Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

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 CO 2. 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:
 [1] ;  [2] ;  [1] ;  [3] ;  [3] ;  [4] ;  [2] ;  [5] ;  [1] ;  [6] ;  [7] ;  [7] ;  [8] ;  [9] ;  [10] ;  [1] ;  [2] ;  [11] ;  [5] ;  [11] more »;  [12] ;  [13] ;  [1] ;  [14] ;  [13] ;  [15] ;  [2] ;  [14] ;  [2] ;  [16] ;  [17] ;  [9] ;  [18] ;  [19] ;  [7] ;  [19] ;  [20] ;  [17] ;  [21] ;  [10] ;  [22] ;  [1] ;  [1] ;  [23] « less
  1. Univ. of East Anglia, Norwich (United Kingdom)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Norwich Research Park (United Kingdom). Earlham Inst.
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  5. Stazione Zoologica Anton Dohrn, Naples (Italy)
  6. Univ. of East Anglia, Norwich (United Kingdom); Norwich Research Park (United Kingdom). Earlham Inst.
  7. J. Craig Venter Inst., La Jolla, CA (United States)
  8. Alfred-Wegener-Institut Helmholtz-Zentrum fur Polar- and Meeresforschung, Bremerhaven (Germany); Hochschule Bremerhaven (Germany)
  9. Univ. Paris-Saclay, Versailles (France)
  10. PSL Research Univ., Paris (France)
  11. Sorbonne Univ., Paris (France)
  12. Univ. of Cologne (Germany); Leibniz Inst. of Freshwater, Ecology and Inland Fisheries, Berlin (Germany)
  13. Univ. Konstanz (Germany)
  14. Medical Univ. of South Carolina, Charleston, SC (United States)
  15. Univ. of Duisburg-Essen (Germany)
  16. Leibniz Inst. fur Biodiversiat der Tiere, Bonn (Germany)
  17. Univ. of Washington, Seattle, WA (United States)
  18. Univ. of Nevada, Las Vegas, NV (United States)
  19. Alfred-Wegener-Institut Helmholtz-Zentrum fur Polar- and Meeresforschung, Bremerhaven (Germany)
  20. Monterey Bay Aquarium Research Inst., Moss Landing, CA (United States)
  21. Univ. of East Anglia, Norwich (United Kingdom); Norwich Research Park (United Kingdom). Earlham Inst.
  22. Univ. of British Columbia, Vancouver, BC (Canada)
  23. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 541; Journal Issue: 7638; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1436620

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., Glockner, 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, van Oosterhout, Cock, and Grigoriev, Igor V.. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. United States: N. p., Web. doi:10.1038/nature20803.
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., Glockner, 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, van Oosterhout, Cock, & Grigoriev, Igor V.. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. United States. doi:10.1038/nature20803.
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., Glockner, 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, van Oosterhout, Cock, and Grigoriev, Igor V.. 2017. "Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus". United States. doi:10.1038/nature20803. https://www.osti.gov/servlets/purl/1436620.
@article{osti_1436620,
title = {Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus},
author = {Mock, Thomas and Otillar, Robert P. and Strauss, Jan and McMullan, Mark and Paajanen, Pirita and Schmutz, Jeremy and Salamov, Asaf and Sanges, Remo and Toseland, Andrew and Ward, Ben J. and Allen, Andrew E. and Dupont, Christopher L. and Frickenhaus, Stephan and Maumus, Florian and Veluchamy, Alaguraj and Wu, Taoyang and Barry, Kerrie W. and Falciatore, Angela and Ferrante, Maria I. and Fortunato, Antonio E. and Glockner, Gernot and Gruber, Ansgar and Hipkin, Rachel and Janech, Michael G. and Kroth, Peter G. and Leese, Florian and Lindquist, Erika A. and Lyon, Barbara R. and Martin, Joel and Mayer, Christoph and Parker, Micaela and Quesneville, Hadi and Raymond, James A. and Uhlig, Christiane and Valas, Ruben E. and Valentin, Klaus U. and Worden, Alexandra Z. and Armbrust, E. Virginia and Clark, Matthew D. and Bowler, Chris and Green, Beverley R. and Moulton, Vincent and van Oosterhout, Cock and Grigoriev, Igor V.},
abstractNote = {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.},
doi = {10.1038/nature20803},
journal = {Nature (London)},
number = 7638,
volume = 541,
place = {United States},
year = {2017},
month = {1}
}

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