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Novel virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA.
Department of Biology, Centre for Geobiology, University of Bergen, N -5020 Bergen, Norway.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
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(English)In: Article in journal (Refereed) Submitted
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-362611OAI: oai:DiVA.org:uu-362611DiVA, id: diva2:1255285
Available from: 2018-10-11 Created: 2018-10-11 Last updated: 2018-10-14Bibliographically approved
In thesis
1. Exploring the diversity and evolution of giant viruses in deep sea sediments using genome-resolved metagenomics
Open this publication in new window or tab >>Exploring the diversity and evolution of giant viruses in deep sea sediments using genome-resolved metagenomics
2018 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Viruses are the most abundant biological entities on this planet, which is impressive considering that they are completely dependent on their hosts for reproduction. Recently the idea of what viruses are has changed dramatically, with the discovery of giant viruses that belong to the Nucleocytoplasmic Large DNA Viruses (NCLDV), such as Mimiviridae, Marseilleviridae, and the proposed families Pandoraviruses, and Pithoviruses. Not only are some of these viruses as large as bacteria in size, their genomes also exceed the size of some prokaryotic genomes. The evolutionary path to viral giganticism is not yet fully understood, and several opposing theories have been proposed. The more examples of giant viruses we have to study, the clearer the picture becomes. The rate of discovery, however, is limited by the low capacity of culturing. In an effort to contribute through culture-independent methods, I used genome-resolved metagenomics to retrieve genomes of 23 new members of the NCLDV from deep sea sediment samples that were taken near Loki’s Castle hydrothermal vent field. This method has previously been used to study uncultured Bacteria and Archaea, but few successful cases of metagenomic binning of NCLDV have been documented. New methods for refinement and quality control of the binned genomes were developed, combining reads profiling with differential coverage binning, and composition-based cleaning of potentially contaminating sequences. The binned genomes represent several novel clades of NCLDV, the most noteworthy ones distantly related to Pithoviruses and Marseilleviridae, and greatly expand their overall diversity. Phylogenetic analysis of their genome content supports the independent evolution of viral giganticism from smaller viruses. Continued use of metagenomics to explore the presence of NCLDV in environmental samples will lead to new insights into their diversity, evolution, and biology.

Place, publisher, year, edition, pages
Uppsala: Uppsala universitet, 2018. p. 38
Keywords
Metagenomics, binning, viruses, NCLDV, Megavirales, viral evolution.
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-363049 (URN)
Presentation
2018-11-28, C8:305, Biomedical centre, Husargatan 3, Uppsala, 14:30 (English)
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Available from: 2018-10-15 Created: 2018-10-14 Last updated: 2018-10-22Bibliographically approved

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Bäckström, DisaDharamshi, JennahHoma, FelixZaremba-Niedzwiedzka, KatarzynaSpang, AnjaEttema, Thijs J. G.

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Molecular EvolutionScience for Life Laboratory, SciLifeLab
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