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Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism.
mBio. 2019 03 05; 10(2)MBIO

Abstract

The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, "Megavirales") include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki's Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki's Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

Authors+Show Affiliations

Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway.Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands. Utrecht University, Den Burg, The Netherlands.National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA koonin@ncbi.nlm.nih.gov thijs.ettema@icm.uu.se.Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden koonin@ncbi.nlm.nih.gov thijs.ettema@icm.uu.se.

Pub Type(s)

Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30837339

Citation

Bäckström, Disa, et al. "Virus Genomes From Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism." MBio, vol. 10, no. 2, 2019.
Bäckström D, Yutin N, Jørgensen SL, et al. Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism. mBio. 2019;10(2).
Bäckström, D., Yutin, N., Jørgensen, S. L., Dharamshi, J., Homa, F., Zaremba-Niedwiedzka, K., Spang, A., Wolf, Y. I., Koonin, E. V., & Ettema, T. J. G. (2019). Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism. MBio, 10(2). https://doi.org/10.1128/mBio.02497-18
Bäckström D, et al. Virus Genomes From Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism. mBio. 2019 03 5;10(2) PubMed PMID: 30837339.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism. AU - Bäckström,Disa, AU - Yutin,Natalya, AU - Jørgensen,Steffen L, AU - Dharamshi,Jennah, AU - Homa,Felix, AU - Zaremba-Niedwiedzka,Katarzyna, AU - Spang,Anja, AU - Wolf,Yuri I, AU - Koonin,Eugene V, AU - Ettema,Thijs J G, Y1 - 2019/03/05/ PY - 2019/3/7/entrez PY - 2019/3/7/pubmed PY - 2019/5/22/medline KW - deep sea sediments KW - giant viruses KW - metagenomics KW - nucleocytoplasmic large DNA viruses KW - virus evolution JF - mBio JO - mBio VL - 10 IS - 2 N2 - The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, "Megavirales") include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki's Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki's Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches. SN - 2150-7511 UR - https://www.unboundmedicine.com/medline/citation/30837339/Virus_Genomes_from_Deep_Sea_Sediments_Expand_the_Ocean_Megavirome_and_Support_Independent_Origins_of_Viral_Gigantism_ L2 - http://mbio.asm.org/cgi/pmidlookup?view=long&pmid=30837339 DB - PRIME DP - Unbound Medicine ER -