@article{RN3,
   author = {Hingamp, P. and Grimsley, N. and Acinas, S. G. and Clerissi, C. and Subirana, L. and Poulain, J. and Ferrera, I. and Sarmento, H. and Villar, E. and Lima-Mendez, G. and Faust, K. and Sunagawa, S. and Claverie, J. M. and Moreau, H. and Desdevises, Y. and Bork, P. and Raes, J. and de Vargas, C. and Karsenti, E. and Kandels-Lewis, S. and Jaillon, O. and Not, F. and Pesant, S. and Wincker, P. and Ogata, H.},
   title = {Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes},
   journal = {ISME J},
   volume = {7},
   number = {9},
   pages = {1678-95},
   note = {Hingamp, Pascal
Grimsley, Nigel
Acinas, Silvia G
Clerissi, Camille
Subirana, Lucie
Poulain, Julie
Ferrera, Isabel
Sarmento, Hugo
Villar, Emilie
Lima-Mendez, Gipsi
Faust, Karoline
Sunagawa, Shinichi
Claverie, Jean-Michel
Moreau, Herve
Desdevises, Yves
Bork, Peer
Raes, Jeroen
de Vargas, Colomban
Karsenti, Eric
Kandels-Lewis, Stefanie
Jaillon, Olivier
Not, Fabrice
Pesant, Stephane
Wincker, Patrick
Ogata, Hiroyuki
eng
Research Support, Non-U.S. Gov't
England
ISME J. 2013 Sep;7(9):1678-95. doi: 10.1038/ismej.2013.59. Epub 2013 Apr 11.},
   abstract = {Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 mum size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.},
   keywords = {Animals
*Biodiversity
Cell Nucleus/virology
Cytoplasm/virology
DNA Viruses/*classification/genetics/*physiology
Eukaryota/virology
Gene Transfer, Horizontal
Genes, Viral/genetics
Genome, Viral/genetics
Indian Ocean
*Metagenome
Oceans and Seas
Oomycetes/virology
Phycodnaviridae/classification/genetics/physiology
Phylogeny
Population Density
Prokaryotic Cells/physiology},
   ISSN = {1751-7370 (Electronic)
1751-7362 (Linking)},
   DOI = {10.1038/ismej.2013.59},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/23575371},
   year = {2013},
   type = {Journal Article}
}

{"_id":"yrWBSHQWTFg5oEeuM","bibbaseid":"hingamp-grimsley-acinas-clerissi-subirana-poulain-ferrera-sarmento-etal-exploringnucleocytoplasmiclargednavirusesintaraoceansmicrobialmetagenomes-2013","downloads":3,"creationDate":"2015-12-07T04:12:15.971Z","title":"Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes","author_short":["Hingamp, P.","Grimsley, N.","Acinas, S. G.","Clerissi, C.","Subirana, L.","Poulain, J.","Ferrera, I.","Sarmento, H.","Villar, E.","Lima-Mendez, G.","Faust, K.","Sunagawa, S.","Claverie, J. M.","Moreau, H.","Desdevises, Y.","Bork, P.","Raes, J.","de Vargas, C.","Karsenti, E.","Kandels-Lewis, S.","Jaillon, O.","Not, F.","Pesant, S.","Wincker, P.","Ogata, H."],"year":2013,"bibtype":"article","biburl":"https://bibbase.org/network/files/CzfdMm64N7sna2FRu","bibdata":{"bibtype":"article","type":"Journal Article","author":[{"propositions":[],"lastnames":["Hingamp"],"firstnames":["P."],"suffixes":[]},{"propositions":[],"lastnames":["Grimsley"],"firstnames":["N."],"suffixes":[]},{"propositions":[],"lastnames":["Acinas"],"firstnames":["S.","G."],"suffixes":[]},{"propositions":[],"lastnames":["Clerissi"],"firstnames":["C."],"suffixes":[]},{"propositions":[],"lastnames":["Subirana"],"firstnames":["L."],"suffixes":[]},{"propositions":[],"lastnames":["Poulain"],"firstnames":["J."],"suffixes":[]},{"propositions":[],"lastnames":["Ferrera"],"firstnames":["I."],"suffixes":[]},{"propositions":[],"lastnames":["Sarmento"],"firstnames":["H."],"suffixes":[]},{"propositions":[],"lastnames":["Villar"],"firstnames":["E."],"suffixes":[]},{"propositions":[],"lastnames":["Lima-Mendez"],"firstnames":["G."],"suffixes":[]},{"propositions":[],"lastnames":["Faust"],"firstnames":["K."],"suffixes":[]},{"propositions":[],"lastnames":["Sunagawa"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Claverie"],"firstnames":["J.","M."],"suffixes":[]},{"propositions":[],"lastnames":["Moreau"],"firstnames":["H."],"suffixes":[]},{"propositions":[],"lastnames":["Desdevises"],"firstnames":["Y."],"suffixes":[]},{"propositions":[],"lastnames":["Bork"],"firstnames":["P."],"suffixes":[]},{"propositions":[],"lastnames":["Raes"],"firstnames":["J."],"suffixes":[]},{"propositions":["de"],"lastnames":["Vargas"],"firstnames":["C."],"suffixes":[]},{"propositions":[],"lastnames":["Karsenti"],"firstnames":["E."],"suffixes":[]},{"propositions":[],"lastnames":["Kandels-Lewis"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Jaillon"],"firstnames":["O."],"suffixes":[]},{"propositions":[],"lastnames":["Not"],"firstnames":["F."],"suffixes":[]},{"propositions":[],"lastnames":["Pesant"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Wincker"],"firstnames":["P."],"suffixes":[]},{"propositions":[],"lastnames":["Ogata"],"firstnames":["H."],"suffixes":[]}],"title":"Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes","journal":"ISME J","volume":"7","number":"9","pages":"1678-95","note":"Hingamp, Pascal Grimsley, Nigel Acinas, Silvia G Clerissi, Camille Subirana, Lucie Poulain, Julie Ferrera, Isabel Sarmento, Hugo Villar, Emilie Lima-Mendez, Gipsi Faust, Karoline Sunagawa, Shinichi Claverie, Jean-Michel Moreau, Herve Desdevises, Yves Bork, Peer Raes, Jeroen de Vargas, Colomban Karsenti, Eric Kandels-Lewis, Stefanie Jaillon, Olivier Not, Fabrice Pesant, Stephane Wincker, Patrick Ogata, Hiroyuki eng Research Support, Non-U.S. Gov't England ISME J. 2013 Sep;7(9):1678-95. doi: 10.1038/ismej.2013.59. Epub 2013 Apr 11.","abstract":"Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 mum size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.","keywords":"Animals *Biodiversity Cell Nucleus/virology Cytoplasm/virology DNA Viruses/*classification/genetics/*physiology Eukaryota/virology Gene Transfer, Horizontal Genes, Viral/genetics Genome, Viral/genetics Indian Ocean *Metagenome Oceans and Seas Oomycetes/virology Phycodnaviridae/classification/genetics/physiology Phylogeny Population Density Prokaryotic Cells/physiology","issn":"1751-7370 (Electronic) 1751-7362 (Linking)","doi":"10.1038/ismej.2013.59","url":"https://www.ncbi.nlm.nih.gov/pubmed/23575371","year":"2013","bibtex":"@article{RN3,\r\n author = {Hingamp, P. and Grimsley, N. and Acinas, S. G. and Clerissi, C. and Subirana, L. and Poulain, J. and Ferrera, I. and Sarmento, H. and Villar, E. and Lima-Mendez, G. and Faust, K. and Sunagawa, S. and Claverie, J. M. and Moreau, H. and Desdevises, Y. and Bork, P. and Raes, J. and de Vargas, C. and Karsenti, E. and Kandels-Lewis, S. and Jaillon, O. and Not, F. and Pesant, S. and Wincker, P. and Ogata, H.},\r\n title = {Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes},\r\n journal = {ISME J},\r\n volume = {7},\r\n number = {9},\r\n pages = {1678-95},\r\n note = {Hingamp, Pascal\r\nGrimsley, Nigel\r\nAcinas, Silvia G\r\nClerissi, Camille\r\nSubirana, Lucie\r\nPoulain, Julie\r\nFerrera, Isabel\r\nSarmento, Hugo\r\nVillar, Emilie\r\nLima-Mendez, Gipsi\r\nFaust, Karoline\r\nSunagawa, Shinichi\r\nClaverie, Jean-Michel\r\nMoreau, Herve\r\nDesdevises, Yves\r\nBork, Peer\r\nRaes, Jeroen\r\nde Vargas, Colomban\r\nKarsenti, Eric\r\nKandels-Lewis, Stefanie\r\nJaillon, Olivier\r\nNot, Fabrice\r\nPesant, Stephane\r\nWincker, Patrick\r\nOgata, Hiroyuki\r\neng\r\nResearch Support, Non-U.S. Gov't\r\nEngland\r\nISME J. 2013 Sep;7(9):1678-95. doi: 10.1038/ismej.2013.59. Epub 2013 Apr 11.},\r\n abstract = {Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 mum size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.},\r\n keywords = {Animals\r\n*Biodiversity\r\nCell Nucleus/virology\r\nCytoplasm/virology\r\nDNA Viruses/*classification/genetics/*physiology\r\nEukaryota/virology\r\nGene Transfer, Horizontal\r\nGenes, Viral/genetics\r\nGenome, Viral/genetics\r\nIndian Ocean\r\n*Metagenome\r\nOceans and Seas\r\nOomycetes/virology\r\nPhycodnaviridae/classification/genetics/physiology\r\nPhylogeny\r\nPopulation Density\r\nProkaryotic Cells/physiology},\r\n ISSN = {1751-7370 (Electronic)\r\n1751-7362 (Linking)},\r\n DOI = {10.1038/ismej.2013.59},\r\n url = {https://www.ncbi.nlm.nih.gov/pubmed/23575371},\r\n year = {2013},\r\n type = {Journal Article}\r\n}\r\n\r\n","author_short":["Hingamp, P.","Grimsley, N.","Acinas, S. 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