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Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism
- Source :
- mBio 10 (2019) 2, mBio, e02497-18, mBio, Vol 10, Iss 2 (2019), mBio, Vol 10, Iss 2, p e02497-18 (2019), mBio, 10(2)
- Publication Year :
- 2018
- Publisher :
- Cold Spring Harbor Laboratory, 2018.
-
Abstract
- 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.<br />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.
- Subjects :
- Geologic Sediments
Marseilleviridae
viruses
nucleocytoplasmic large DNA viruses
Ecological and Evolutionary Science
deep sea sediments
Genome, Viral
Biology
Nucleocytoplasmic large DNA viruses
Microbiology
Genome
Evolutionsbiologi
03 medical and health sciences
Hydrothermal Vents
Virology
Mimiviridae
Giant Virus
14. Life underwater
Atlantic Ocean
Phylogeny
Giant viruses
030304 developmental biology
virus evolution
Evolutionary Biology
0303 health sciences
metagenomics
Phylogenetic tree
030306 microbiology
Genetic Variation
Deep sea sediments
Sequence Analysis, DNA
biology.organism_classification
Virus evolution
QR1-502
Evolutionary biology
Metagenomics
Viral evolution
Giant Viruses
DNA, Viral
Phycodnaviridae
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 21612129
- Database :
- OpenAIRE
- Journal :
- mBio 10 (2019) 2, mBio, e02497-18, mBio, Vol 10, Iss 2 (2019), mBio, Vol 10, Iss 2, p e02497-18 (2019), mBio, 10(2)
- Accession number :
- edsair.doi.dedup.....3a3b7d4d97bc1d5c4c709ca7ea31067e
- Full Text :
- https://doi.org/10.1101/469403