Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, 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 ORCID: https://orcid.org/0000-0002-2663-2001, 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 ORCID: https://orcid.org/0000-0001-9371-6435, van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X and Grigoriev, Igor V. (2017) Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus. Nature, 541. 536–540. ISSN 0028-0836

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Abstract

The Southern Ocean houses a diverse and productive community of organisms1, 2. 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 ice3, 4, 5, 6, 7. 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 cylindrus8, 9, 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.

Item Type:	Article
Additional Information:	Acknowledgements: The authors 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.
Faculty \ School:	Faculty of Science > School of Environmental Sciences Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Environmental Biology Faculty of Science > Research Groups > Resources, Sustainability and Governance (former - to 2018) Faculty of Science > Research Groups > Marine and Atmospheric Sciences (former - to 2017) Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre Faculty of Science > Research Groups > Data Science and AI
Depositing User:	Pure Connector
Date Deposited:	23 Jan 2017 21:32
Last Modified:	10 Dec 2024 01:29
URI:	https://ueaeprints.uea.ac.uk/id/eprint/62155
DOI:	10.1038/nature20803

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