The Giant Cafeteria roenbergensis Virus That Infects a Widespread Marine Phagocytic Protist Is a New Member of the Fourth Domain of Life
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{"title"=>"The giant Cafeteria roenbergensis virus that infects a widespread marine phagocytic protist is a new member of the fourth domain of life", "type"=>"journal", "authors"=>[{"first_name"=>"Philippe", "last_name"=>"Colson", "scopus_author_id"=>"7102090499"}, {"first_name"=>"Gregory", "last_name"=>"Gimenez", "scopus_author_id"=>"35810067900"}, {"first_name"=>"Mickaël", "last_name"=>"Boyer", "scopus_author_id"=>"23487817100"}, {"first_name"=>"Ghislain", "last_name"=>"Fournous", "scopus_author_id"=>"6506000654"}, {"first_name"=>"Didier", "last_name"=>"Raoult", "scopus_author_id"=>"36040059800"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361726197", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0018935", "scopus"=>"2-s2.0-79955747671", "pmid"=>"21559486", "sgr"=>"79955747671"}, "id"=>"9615c4a2-ccad-372b-8333-2faef4923e34", "abstract"=>"BACKGROUND: A recent work has provided strong arguments in favor of a fourth domain of Life composed of nucleo-cytoplasmic large DNA viruses (NCLDVs). This hypothesis was supported by phylogenetic and phyletic analyses based on a common set of proteins conserved in Eukarya, Archaea, Bacteria, and viruses, and implicated in the functions of information storage and processing. Recently, the genome of a new NCLDV, Cafeteria roenbergensis virus (CroV), was released. The present work aimed to determine if CroV supports the fourth domain of Life hypothesis.\\n\\nMETHODS: A consensus phylogenetic tree of NCLDVs including CroV was generated from a concatenated alignment of four universal proteins of NCLDVs. Some features of the gene complement of CroV and its distribution along the genome were further analyzed. Phylogenetic and phyletic analyses were performed using the previously identified common set of informational genes present in Eukarya, Archaea, Bacteria, and NCLDVs, including CroV.\\n\\nFINDINGS: Phylogenetic reconstructions indicated that CroV is clearly related to the Mimiviridae family. The comparison between the gene repertoires of CroV and Mimivirus showed similarities regarding the gene contents and genome organization. In addition, the phyletic clustering based on the comparison of informational gene repertoire between Eukarya, Archaea, Bacteria, and NCLDVs unambiguously classified CroV with other NCLDVs and clearly included it in a fourth domain of Life. Taken together, these data suggest that Mimiviridae, including CroV, may have inherited a common gene content probably acquired from a common Mimiviridae ancestor.\\n\\nCONCLUSIONS: This further analysis of the gene repertoire of CroV consolidated the fourth domain of Life hypothesis and contributed to outline a functional pan-genome for giant viruses infecting phagocytic protistan grazers.", "link"=>"http://www.mendeley.com/research/giant-cafeteria-roenbergensis-virus-infects-widespread-marine-phagocytic-protist-new-member-fourth-d", "reader_count"=>100, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>4, "Researcher"=>24, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>1, "Student > Master"=>11, "Other"=>4, "Student > Bachelor"=>16, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>4, "Researcher"=>24, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>1, "Student > Master"=>11, "Other"=>4, "Student > Bachelor"=>16, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>12, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>70, "Medicine and Dentistry"=>1, "Chemistry"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>70}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>12}, "Environmental Science"=>{"Environmental Science"=>5}}, "reader_count_by_country"=>{"United States"=>3, "United Kingdom"=>3, "Thailand"=>1, "Portugal"=>1, "Spain"=>2, "Canada"=>1, "Austria"=>1, "Norway"=>1, "South Africa"=>1, "Mexico"=>1, "Lithuania"=>1, "Australia"=>1, "Germany"=>2}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/778176"], "description"=>"<p>ORFs that form pairs of reciprocal best BLASTp hits with ORFs of Mimivirus, Marseillevirus, <i>Paramecium bursaria Chlorella</i> virus 1, Vaccinia virus, or <i>Acanthamoeba castellanii</i>, and duplicated genes. RBH, reciprocal best BLASTp hits.</p>", "links"=>[], "tags"=>["orfs", "crov", "genome", "618"], "article_id"=>448542, "categories"=>["Virology", "Evolutionary Biology"], "users"=>["Philippe Colson", "Grégory Gimenez", "Mickaël Boyer", "Ghislain Fournous", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018935.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_map_of_the_distribution_of_ORFs_along_the_CroV_genome_sequenced_fragment_618_kb_/448542", "title"=>"Genome map of the distribution of ORFs along the CroV genome (sequenced fragment, 618 kb).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-29 02:22:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/778266"], "description"=>"<p>The MCP phylogenetic tree was inferred with Bayesian approach from a cured alignment of 24 sequences (132 conserved positions) from the NCLDV families, from the <i>A. castellanii</i> capsid homolog fragment, and from the <i>Ectocarpus siliculosus</i> capsid homolog. Poxviruses capsid proteins were not included in the tree as their sequences are too divergent from those of other NCLDV families. Bayesian posterior probabilities are mentioned near branches as a percentage and are used as confidence values of tree branches. Scale bar represents the number of estimated changes per position for a unit of branch length. Abbreviations: APMV, <i>A. polyphaga</i> mimivirus; ASFV, African swine fever virus; ATCV-1, <i>Acanthocystis turfacea</i> chlorella virus 1; CeV, <i>C. ericina</i> virus 01; CIV, Chilo iridiscent virus; CroV, <i>C. roenbergensis</i> virus; DpAV4, <i>Diadromus pulchellus</i> ascovirus 4a; EhV-86, <i>E. huxleyi</i> virus 86; ESV-1, <i>Ectocarpus siliculosus</i> virus 1; FirrV-1, <i>Feldmannia irregularis</i> virus 1; FV3, Frog virus 3; HaV, <i>H. akashiwo</i> virus 01; HvAV3, <i>Heliothis virescens</i> ascovirus 3e; IIV-3, Invertebrate iridiscent virus 3; ISKNV, Infectious spleen and kidney necrosis virus; LDV, Lymphocystis disease virus; MarV, Marseillevirus; OtV-5, <i>Ostreococcus tauri</i> virus 5; PBCV-1, <i>P. bursarium</i> chlorella virus 1; PoV, <i>P. orientalis</i> virus 01; PpV, <i>P. pouchetti</i> virus 01; TnAV2, <i>Trichoplusia ni</i> ascovirus 2c. GI numbers are listed next to abbreviations of corresponding taxonomic name of each virus.</p>", "links"=>[], "tags"=>["ncldv", "capsid"], "article_id"=>448634, "categories"=>["Virology", "Evolutionary Biology"], "users"=>["Philippe Colson", "Grégory Gimenez", "Mickaël Boyer", "Ghislain Fournous", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018935.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_the_NCLDV_major_capsid_protein_MCP_/448634", "title"=>"Phylogenetic tree of the NCLDV major capsid protein (MCP).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-29 02:23:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/778405"], "description"=>"<p>Bayesian posterior probabilities are mentioned near branches and are used as confidence values of tree branches. A color code was used to represent taxonomic groups, <i>Archaea</i> in green, <i>Eukarya</i> in blue, NCLDVs in red, and environmental sequences in black. For details on evolutionary models and phylogenetic methods, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018935#s4\" target=\"_blank\">Materials and Methods</a>.</p>", "links"=>[], "tags"=>["ii", "phylogenetic", "97", "constructed", "bayesian"], "article_id"=>448775, "categories"=>["Virology", "Evolutionary Biology"], "users"=>["Philippe Colson", "Grégory Gimenez", "Mickaël Boyer", "Ghislain Fournous", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018935.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TFIIB_transcription_factor_II_B_phylogenetic_tree_82_sequences_97_positions_constructed_using_a_Bayesian_approach_/448775", "title"=>"TFIIB (transcription factor II B) phylogenetic tree (82 sequences, 97 positions) constructed using a Bayesian approach.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-29 02:26:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/390815", "https://ndownloader.figshare.com/files/390865", "https://ndownloader.figshare.com/files/390929", "https://ndownloader.figshare.com/files/390997", "https://ndownloader.figshare.com/files/391048", "https://ndownloader.figshare.com/files/391121", "https://ndownloader.figshare.com/files/391169", "https://ndownloader.figshare.com/files/391205", "https://ndownloader.figshare.com/files/391245", "https://ndownloader.figshare.com/files/391301", "https://ndownloader.figshare.com/files/391342", "https://ndownloader.figshare.com/files/391401", "https://ndownloader.figshare.com/files/391449", "https://ndownloader.figshare.com/files/391517", "https://ndownloader.figshare.com/files/391548", "https://ndownloader.figshare.com/files/391582"], "description"=>"<div><h3>Background</h3><p>A recent work has provided strong arguments in favor of a fourth domain of Life composed of nucleo-cytoplasmic large DNA viruses (NCLDVs). This hypothesis was supported by phylogenetic and phyletic analyses based on a common set of proteins conserved in <em>Eukarya</em>, <em>Archaea</em>, <em>Bacteria</em>, and viruses, and implicated in the functions of information storage and processing. Recently, the genome of a new NCLDV, <em>Cafeteria roenbergensis virus</em> (CroV), was released. The present work aimed to determine if CroV supports the fourth domain of Life hypothesis.</p> <h3>Methods</h3><p>A consensus phylogenetic tree of NCLDVs including CroV was generated from a concatenated alignment of four universal proteins of NCLDVs. Some features of the gene complement of CroV and its distribution along the genome were further analyzed. Phylogenetic and phyletic analyses were performed using the previously identified common set of informational genes present in <em>Eukarya</em>, <em>Archaea</em>, <em>Bacteria</em>, and NCLDVs, including CroV.</p> <h3>Findings</h3><p>Phylogenetic reconstructions indicated that CroV is clearly related to the <em>Mimiviridae</em> family. The comparison between the gene repertoires of CroV and Mimivirus showed similarities regarding the gene contents and genome organization. In addition, the phyletic clustering based on the comparison of informational gene repertoire between <em>Eukarya</em>, <em>Archaea</em>, <em>Bacteria</em>, and NCLDVs unambiguously classified CroV with other NCLDVs and clearly included it in a fourth domain of Life. Taken together, these data suggest that <em>Mimiviridae</em>, including CroV, may have inherited a common gene content probably acquired from a common <em>Mimiviridae</em> ancestor.</p> <h3>Conclusions</h3><p>This further analysis of the gene repertoire of CroV consolidated the fourth domain of Life hypothesis and contributed to outline a functional pan-genome for giant viruses infecting phagocytic protistan grazers.</p> </div>", "links"=>[], "tags"=>["infects", "phagocytic", "Protist"], "article_id"=>137204, "categories"=>["Cancer", "Evolutionary Biology"], "users"=>["Philippe Colson", "Grégory Gimenez", "Mickaël Boyer", "Ghislain Fournous", "Didier Raoult"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0018935.s001", "https://dx.doi.org/10.1371/journal.pone.0018935.s002", "https://dx.doi.org/10.1371/journal.pone.0018935.s003", "https://dx.doi.org/10.1371/journal.pone.0018935.s004", "https://dx.doi.org/10.1371/journal.pone.0018935.s005", "https://dx.doi.org/10.1371/journal.pone.0018935.s006", "https://dx.doi.org/10.1371/journal.pone.0018935.s007", "https://dx.doi.org/10.1371/journal.pone.0018935.s008", "https://dx.doi.org/10.1371/journal.pone.0018935.s009", "https://dx.doi.org/10.1371/journal.pone.0018935.s010", "https://dx.doi.org/10.1371/journal.pone.0018935.s011", "https://dx.doi.org/10.1371/journal.pone.0018935.s012", "https://dx.doi.org/10.1371/journal.pone.0018935.s013", "https://dx.doi.org/10.1371/journal.pone.0018935.s014", "https://dx.doi.org/10.1371/journal.pone.0018935.s015", "https://dx.doi.org/10.1371/journal.pone.0018935.s016"], "stats"=>{"downloads"=>13, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Giant_Cafeteria_roenbergensis_Virus_That_Infects_a_Widespread_Marine_Phagocytic_Protist_Is_a_New_Member_of_the_Fourth_Domain_of_Life/137204", "title"=>"The Giant <em>Cafeteria roenbergensis</em> Virus That Infects a Widespread Marine Phagocytic Protist Is a New Member of the Fourth Domain of Life", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-04-29 02:00:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/778064"], "description"=>"<p>COG functional categories, NCLDV core genes (classes I–III), and NCVOGs.</p>", "links"=>[], "tags"=>["orfs", "crov", "genome", "618"], "article_id"=>448433, "categories"=>["Virology", "Evolutionary Biology"], "users"=>["Philippe Colson", "Grégory Gimenez", "Mickaël Boyer", "Ghislain Fournous", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018935.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_map_of_the_distribution_of_ORFs_along_the_CroV_genome_sequenced_fragment_618_kb_/448433", "title"=>"Genome map of the distribution of ORFs along the CroV genome (sequenced fragment, 618 kb).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-29 02:20:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/778693"], "description"=>"<p>Green, presence; red, absence. <i>Abbreviated names for NCLDVs</i>: b1_Helvi, Heliothis virescens ascovirus 3e; b1_Spofr, Spodoptera frugiperda ascovirus 1a; b1_Trini, Trichoplusia ni ascovirus 2c; c1_Afrsw, African swine fever virus; l1_Aedta, Aedes taeniorhynchus iridescent virus (Invertebrate iridescent virus 3); l2_Invir, Invertebrate iridescent virus 6; l3_Lymch, Lymphocystis disease virus - isolate China; l3_Lymdi, Lymphocystis disease virus 1; l4_Infsp, Infectious spleen and kidney necrosis virus; l5_Ambti, Ambystoma tigrinum virus; l5_Frovi, Frog virus 3; l5_Singr, Singapore grouper iridovirus; m6_Masvi, Marseille virus; n1_Acapo, Acanthamoeba polyphaga mimivirus; n2_Mamav, Mamavirus; q1_Acatu, Acanthocystis turfacea Chlorella virus 1; q1_ParAR, Paramecium bursaria Chlorella virus AR158; q1_Parbu, Paramecium bursaria Chlorella virus 1; q1_ParFR, Paramecium bursaria Chlorella virus FR483; q1_ParMT, Paramecium bursaria chlorella virus MT325; q1_ParNY, Paramecium bursaria Chlorella virus NY2A; q2_Emihu, Emiliania huxleyi virus 86; q3_Ectsi, Ectocarpus siliculosus virus 1; q3_Felsp, Feldmannia species virus; q6_Ostvi, Ostreococcus virus OsV5; u1_Bovpa, Bovine papular stomatitis virus; u1_Canvi, Canarypox virus; u1_Crovi, Crocodilepox virus; u1_Deevi, Deerpox virus W-848-83; u1_Fowvi, Fowlpox virus; u1_Goavi, Goatpox virus Pellor; u1_Lumsk, Lumpy skin disease virus NI-2490; u1_Molco, Molluscum contagiosum virus; u1_Myxvi, Myxoma virus; u1_Orfvi, Orf virus, complete genome; u1_Rabfi, Rabbit fibroma virus; u1_Shevi, Sheeppox virus 17077-99; u1_Swivi, Swinepox virus; u1_Tanvi, Tanapox virus; u1_Vacvi, Vaccinia virus; u1_Varvi, Variola virus (smallpox virus); u1_Yabli, Yaba-like disease virus; u1_Yabmo, Yaba monkey tumor virus; u2_Amsmo, Amsacta moorei entomopoxvirus; u2_Melsa, Melanoplus sanguinipes entomopoxvirus.</p>", "links"=>[], "tags"=>["built", "hierarchical", "clustering", "euclidean", "computed", "matrix", "cogs", "ncldv"], "article_id"=>449057, "categories"=>["Virology", "Evolutionary Biology"], "users"=>["Philippe Colson", "Grégory Gimenez", "Mickaël Boyer", "Ghislain Fournous", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018935.g007", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_built_from_the_hierarchical_clustering_on_the_Euclidean_distance_computed_from_a_presence_absence_matrix_based_on_COGs_at_least_present_in_one_NCLDV_genome_/449057", "title"=>"Heatmap built from the hierarchical clustering on the Euclidean distance computed from a presence/absence matrix based on COGs at least present in one NCLDV genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-29 02:30:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/778556"], "description"=>"<p>The phyletic patterns of the putative orthologous sets of informational genes indicating the presence/absence of the respective gene in each cellular organism and virus were used for the construction of the dendogram tree. For details, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018935#s4\" target=\"_blank\">Materials and Methods</a>. A color code was used to represent taxonomic groups, <i>Bacteria</i> in purple, <i>Archaea</i> in green, <i>Eukarya</i> in blue, and NCLDVs in red.</p>", "links"=>[], "tags"=>["clustering", "ncldvs", "phyletic"], "article_id"=>448927, "categories"=>["Virology", "Evolutionary Biology"], "users"=>["Philippe Colson", "Grégory Gimenez", "Mickaël Boyer", "Ghislain Fournous", "Didier Raoult"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018935.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustering_of_Eukarya_Bacteria_Archaea_and_NCLDVs_by_phyletic_patterns_/448927", "title"=>"Hierarchical clustering of <i>Eukarya</i>, <i>Bacteria</i>, <i>Archaea</i> and NCLDVs by phyletic patterns.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-29 02:28:47"}

PMC Usage Stats | Further Information

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