Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club
International audience Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, include giant viruses of Acanthamoeba that were discovered over the last 12 years and are bona fide microbes. Phylogenies based on a few genes conserved amongst these megaviruses and sha...
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ftunivaixmarseil:oai:HAL:hal-01304145v1 2024-05-19T07:47:14+00:00 Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club Sharma, Vikas Colson, Philippe Chabrol, Olivier Pontarotti, Pierre Raoult, Didier Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48 Institut des sciences biologiques - CNRS Biologie (INSB-CNRS)-Institut des sciences biologiques - CNRS Biologie (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut de Mathématiques de Marseille (I2M) Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS) Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille) 2015-08 https://hal.science/hal-01304145 https://hal.science/hal-01304145/document https://hal.science/hal-01304145/file/fmicb-06-00722.pdf https://doi.org/10.3389/fmicb.2015.00722 en eng HAL CCSD Frontiers Media info:eu-repo/semantics/altIdentifier/doi/10.3389/fmicb.2015.00722 info:eu-repo/semantics/altIdentifier/pmid/26300849 hal-01304145 https://hal.science/hal-01304145 https://hal.science/hal-01304145/document https://hal.science/hal-01304145/file/fmicb-06-00722.pdf doi:10.3389/fmicb.2015.00722 PUBMED: 26300849 PUBMEDCENTRAL: PMC4523831 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1664-302X EISSN: 1664-302X Frontiers in Microbiology https://hal.science/hal-01304145 Frontiers in Microbiology, 2015, 6, pp.722. ⟨10.3389/fmicb.2015.00722⟩ Megavirales Pithovirus sibericum Domains of life Giant virus Informational genes Phylogeny Nucleocytoplasmic large DNA viruses TRUC [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology info:eu-repo/semantics/article Journal articles 2015 ftunivaixmarseil https://doi.org/10.3389/fmicb.2015.00722 2024-05-02T00:10:04Z International audience Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, include giant viruses of Acanthamoeba that were discovered over the last 12 years and are bona fide microbes. Phylogenies based on a few genes conserved amongst these megaviruses and shared by microbes classified as Eukarya, Bacteria, and Archaea, allowed for delineation of a fourth monophylogenetic group or "TRUC" (Things Resisting Uncompleted Classification) composed of the Megavirales representatives. A new Megavirales member named Pithovirus sibericum was isolated from a >30,000-year-old dated Siberian permafrost sample. This virion is as large as recently described pandoraviruses but has a genome that is approximately three to four times shorter. Our objective was to update the classification of P. sibericum as a new member of the "Fourth TRUC" club. Phylogenetic trees were constructed based on four conserved ancient genes and a phyletic analysis was concurrently conducted based on the presence/absence patterns of a set of informational genes from members of Megavirales, Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on the four conserved genes revealed that P. sibericum is part of the fourth TRUC composed of Megavirales members, and is closely related to the families Marseilleviridae and Ascoviridae/Iridoviridae. Additionally, hierarchical clustering delineated four branches, and showed that P. sibericum is part of this fourth TRUC. Overall, phylogenetic and phyletic analyses using informational genes clearly indicate that P. sibericum is a new bona fide member of the "Fourth TRUC" club composed of representatives of Megavirales, alongside Bacteria, Archaea, and Eukarya. Article in Journal/Newspaper permafrost Aix-Marseille Université: HAL Frontiers in Microbiology 6 |
institution |
Open Polar |
collection |
Aix-Marseille Université: HAL |
op_collection_id |
ftunivaixmarseil |
language |
English |
topic |
Megavirales Pithovirus sibericum Domains of life Giant virus Informational genes Phylogeny Nucleocytoplasmic large DNA viruses TRUC [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology |
spellingShingle |
Megavirales Pithovirus sibericum Domains of life Giant virus Informational genes Phylogeny Nucleocytoplasmic large DNA viruses TRUC [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology Sharma, Vikas Colson, Philippe Chabrol, Olivier Pontarotti, Pierre Raoult, Didier Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club |
topic_facet |
Megavirales Pithovirus sibericum Domains of life Giant virus Informational genes Phylogeny Nucleocytoplasmic large DNA viruses TRUC [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology |
description |
International audience Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, include giant viruses of Acanthamoeba that were discovered over the last 12 years and are bona fide microbes. Phylogenies based on a few genes conserved amongst these megaviruses and shared by microbes classified as Eukarya, Bacteria, and Archaea, allowed for delineation of a fourth monophylogenetic group or "TRUC" (Things Resisting Uncompleted Classification) composed of the Megavirales representatives. A new Megavirales member named Pithovirus sibericum was isolated from a >30,000-year-old dated Siberian permafrost sample. This virion is as large as recently described pandoraviruses but has a genome that is approximately three to four times shorter. Our objective was to update the classification of P. sibericum as a new member of the "Fourth TRUC" club. Phylogenetic trees were constructed based on four conserved ancient genes and a phyletic analysis was concurrently conducted based on the presence/absence patterns of a set of informational genes from members of Megavirales, Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on the four conserved genes revealed that P. sibericum is part of the fourth TRUC composed of Megavirales members, and is closely related to the families Marseilleviridae and Ascoviridae/Iridoviridae. Additionally, hierarchical clustering delineated four branches, and showed that P. sibericum is part of this fourth TRUC. Overall, phylogenetic and phyletic analyses using informational genes clearly indicate that P. sibericum is a new bona fide member of the "Fourth TRUC" club composed of representatives of Megavirales, alongside Bacteria, Archaea, and Eukarya. |
author2 |
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48 Institut des sciences biologiques - CNRS Biologie (INSB-CNRS)-Institut des sciences biologiques - CNRS Biologie (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut de Mathématiques de Marseille (I2M) Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS) Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille) |
format |
Article in Journal/Newspaper |
author |
Sharma, Vikas Colson, Philippe Chabrol, Olivier Pontarotti, Pierre Raoult, Didier |
author_facet |
Sharma, Vikas Colson, Philippe Chabrol, Olivier Pontarotti, Pierre Raoult, Didier |
author_sort |
Sharma, Vikas |
title |
Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club |
title_short |
Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club |
title_full |
Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club |
title_fullStr |
Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club |
title_full_unstemmed |
Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club |
title_sort |
pithovirus sibericum, a new bona fide member of the "fourth truc" club |
publisher |
HAL CCSD |
publishDate |
2015 |
url |
https://hal.science/hal-01304145 https://hal.science/hal-01304145/document https://hal.science/hal-01304145/file/fmicb-06-00722.pdf https://doi.org/10.3389/fmicb.2015.00722 |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
ISSN: 1664-302X EISSN: 1664-302X Frontiers in Microbiology https://hal.science/hal-01304145 Frontiers in Microbiology, 2015, 6, pp.722. ⟨10.3389/fmicb.2015.00722⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.3389/fmicb.2015.00722 info:eu-repo/semantics/altIdentifier/pmid/26300849 hal-01304145 https://hal.science/hal-01304145 https://hal.science/hal-01304145/document https://hal.science/hal-01304145/file/fmicb-06-00722.pdf doi:10.3389/fmicb.2015.00722 PUBMED: 26300849 PUBMEDCENTRAL: PMC4523831 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.3389/fmicb.2015.00722 |
container_title |
Frontiers in Microbiology |
container_volume |
6 |
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1799487573692776448 |