A phylogenomic framework for charting the diversity and evolution of giant viruses.
Journal
PLoS biology
ISSN: 1545-7885
Titre abrégé: PLoS Biol
Pays: United States
ID NLM: 101183755
Informations de publication
Date de publication:
10 2021
10 2021
Historique:
received:
04
06
2021
accepted:
29
09
2021
revised:
08
11
2021
pubmed:
28
10
2021
medline:
15
12
2021
entrez:
27
10
2021
Statut:
epublish
Résumé
Large DNA viruses of the phylum Nucleocytoviricota have recently emerged as important members of ecosystems around the globe that challenge traditional views of viral complexity. Numerous members of this phylum that cannot be classified within established families have recently been reported, and there is presently a strong need for a robust phylogenomic and taxonomic framework for these viruses. Here, we report a comprehensive phylogenomic analysis of the Nucleocytoviricota, present a set of giant virus orthologous groups (GVOGs) together with a benchmarked reference phylogeny, and delineate a hierarchical taxonomy within this phylum. We show that the majority of Nucleocytoviricota diversity can be partitioned into 6 orders, 32 families, and 344 genera, substantially expanding the number of currently recognized taxonomic ranks for these viruses. We integrate our results within a taxonomy that has been adopted for all viruses to establish a unifying framework for the study of Nucleocytoviricota diversity, evolution, and environmental distribution.
Identifiants
pubmed: 34705818
doi: 10.1371/journal.pbio.3001430
pii: PBIOLOGY-D-21-01459
pmc: PMC8575486
doi:
Substances chimiques
Genetic Markers
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e3001430Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist
Références
J Virol. 2010 Dec;84(24):12555-63
pubmed: 20861243
Viruses. 2021 Jan 20;13(2):
pubmed: 33498458
Nature. 2020 Feb;578(7795):432-436
pubmed: 31968354
Nature. 2020 Dec;588(7836):141-145
pubmed: 33208937
Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19508-13
pubmed: 20974979
Intervirology. 2010;53(5):284-92
pubmed: 20551680
Mol Biol Evol. 2021 Aug 26;:
pubmed: 34436605
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
Bioinformatics. 2018 Mar 15;34(6):1053-1055
pubmed: 29091997
Nat Commun. 2018 Feb 27;9(1):749
pubmed: 29487281
Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17486-91
pubmed: 21987820
Adv Virus Res. 2019;103:167-202
pubmed: 30635076
Elife. 2018 Mar 27;7:
pubmed: 29582753
BMC Bioinformatics. 2011 Apr 28;12:124
pubmed: 21526987
Cell. 2021 Aug 5;184(16):4237-4250.e19
pubmed: 34297924
J Virol. 2011 May;85(9):4520-9
pubmed: 21289127
Science. 2017 Apr 7;356(6333):82-85
pubmed: 28386012
Microbes Environ. 2018 Jul 4;33(2):162-171
pubmed: 29806626
Sci Rep. 2020 Mar 12;10(1):4620
pubmed: 32165658
Mol Syst Biol. 2011 Oct 11;7:539
pubmed: 21988835
Virology. 2014 Oct;466-467:60-70
pubmed: 25035289
Virus Res. 2006 Apr;117(1):156-84
pubmed: 16494962
Curr Opin Microbiol. 2016 Jun;31:50-57
pubmed: 26999382
Virol J. 2005 Aug 16;2:62
pubmed: 16105173
Nat Biotechnol. 2018 Nov;36(10):996-1004
pubmed: 30148503
Front Microbiol. 2021 Jun 07;12:683294
pubmed: 34163457
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Front Microbiol. 2021 Mar 15;12:657471
pubmed: 33790885
Science. 2004 Nov 19;306(5700):1344-50
pubmed: 15486256
Biol Direct. 2012 Oct 04;7:34
pubmed: 23036091
Genome Res. 2009 Aug;19(8):1441-9
pubmed: 19451591
mSystems. 2021 Aug 31;6(4):e0029321
pubmed: 34254826
J Virol. 2017 Jun 26;91(14):
pubmed: 28446675
Virus Evol. 2020 Nov 30;6(2):veaa059
pubmed: 33686356
Nature. 2013 May 16;497(7449):327-31
pubmed: 23657258
Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19585-19592
pubmed: 31506349
Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21848-53
pubmed: 20007369
Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5327-35
pubmed: 26351664
Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10800-5
pubmed: 23754393
Nat Struct Mol Biol. 2021 May;28(5):413-417
pubmed: 33927388
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Biol Direct. 2013 Oct 23;8:25
pubmed: 24148757
Science. 2005 Aug 12;309(5737):1090-2
pubmed: 16099989
Mol Biol Evol. 2014 May;31(5):1261-71
pubmed: 24509691
Nucleic Acids Res. 2018 Jan 4;46(D1):D708-D717
pubmed: 29040670
Viruses. 2019 Dec 23;12(1):
pubmed: 31878033
Mol Biol Evol. 2018 Feb 1;35(2):518-522
pubmed: 29077904
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419
pubmed: 33125078
Nat Commun. 2018 Nov 19;9(1):4881
pubmed: 30451857
Virol J. 2008 Jan 23;5:12
pubmed: 18215256
Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):6040-6045
pubmed: 29784828
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
Syst Biol. 2013 Jan 1;62(1):162-6
pubmed: 22962004
Microbiol Mol Biol Rev. 2020 Mar 4;84(2):
pubmed: 32132243
mBio. 2020 Jan 14;11(1):
pubmed: 31937645
Viruses. 2017 Mar 17;9(3):
pubmed: 28304329
Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20574-20583
pubmed: 31548428
Nat Rev Microbiol. 2008 Apr;6(4):315-9
pubmed: 18311164
J Virol. 2019 Apr 3;93(8):
pubmed: 30728258
Virol J. 2012 Aug 14;9:161
pubmed: 22891861
F1000Res. 2018 Nov 22;7:
pubmed: 30542614
Curr Biol. 2020 Dec 21;30(24):4910-4920.e5
pubmed: 33065010
Viruses. 2017 Mar 15;9(3):
pubmed: 28294997
Nat Commun. 2020 Apr 6;11(1):1710
pubmed: 32249765
Philos Trans R Soc Lond B Biol Sci. 2019 Nov 25;374(1786):20190086
pubmed: 31587639
mBio. 2019 Mar 5;10(2):
pubmed: 30837339
J Virol. 2001 Dec;75(23):11720-34
pubmed: 11689653
Virology. 2018 May;518:423-433
pubmed: 29649682
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842
Virol J. 2009 Dec 17;6:223
pubmed: 20017929
Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4274-9
pubmed: 24591590
Science. 2013 Jul 19;341(6143):281-6
pubmed: 23869018