Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy

The Journal of General Virology
Pakorn AiewsakunPeter Simmonds

Abstract

Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of eukaryotic viruses. Eukaryotic virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of eukaryotic viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipot...Continue Reading

References

Sep 29, 1971·Nature: New Biology·A Hellman, A K Fowler
Jul 27, 2002·Journal of Bacteriology·Forest Rohwer, Rob Edwards
Aug 10, 2002·Journal of Bacteriology·Jeffrey G LawrenceRoger W Hendrix
Oct 19, 2004·Journal of Bacteriology·Daniel Nelson
Nov 8, 2005·Current Opinion in Structural Biology·Dennis H BamfordDavid I Stuart
Sep 21, 2006·Biology Direct·Eugene V KooninValerian V Dolja
Feb 1, 2008·Molecular Biology and Evolution·Gipsi Lima-MendezRaphaël Leplae
Mar 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Katsuhiko S MurakamiLucia B Rothman-Denes
Nov 15, 2008·Nature Reviews. Microbiology·Mart Krupovic, Dennis H Bamford
Oct 28, 2009·BMC Microbiology·Rob LavigneAndrew M Kropinski
Nov 26, 2009·Nucleic Acids Research·Raphaël LeplaeAriane Toussaint
Apr 1, 2011·Journal of Virology·Edward C Holmes
Jul 20, 2011·Research in Microbiology·Gipsi Lima-MendezRaphael Leplae
Oct 29, 2011·Current Opinion in Virology·Graham F Hatfull, Roger W Hendrix
Jan 25, 2012·Archives of Virology·David Prangishvili, Mart Krupovic
Jul 4, 2012·Archives of Virology·H-W Ackermann, D Prangishvili
Mar 4, 2014·The Journal of Microbiology·Ryland Young
Dec 4, 2014·Virology·Evelien M AdriaenssensAndrew M Kropinski
Aug 19, 2015·Proceedings of the National Academy of Sciences of the United States of America·Bo HuJun Liu
Jan 18, 2016·Trends in Microbiology·Eduardo CorelEric Bapteste
Mar 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Moh Lan YapMichael G Rossmann
Aug 18, 2016·Nature·David Paez-EspinoNikos C Kyrpides
Jan 4, 2017·Archives of Virology·Evelien M AdriaenssensJens H Kuhn
Jan 13, 2017·Archives of Virology·Michael J AdamsAndrew J Davison
Jan 31, 2017·Nature Reviews. Microbiology·Peter SimmondsF Murilo Zerbini
Apr 30, 2017·Communicative & Integrative Biology·Jaime IranzoEugene V Koonin
Jul 12, 2017·Nature Microbiology·Travis N Mavrich, Graham F Hatfull
Aug 17, 2017·Cell Reports·Vorrapon ChaikeeratisakJoe Pogliano
Nov 28, 2017·Virus Research·Mart KrupovicEugene V Koonin
Jan 23, 2018·Archives of Virology·Evelien M AdriaenssensJ Rodney Brister

❮ Previous
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Citations

Mar 1, 2019·Viruses·Cynthia Maria ChibaniHeiko Liesegang
May 8, 2019·Viruses·Franziska HufskyManja Marz
May 28, 2019·Systematic Biology·Jakub BarylskiEvelien M Adriaenssens
Apr 7, 2019·EMBO Reports·Iain D Hay, Trevor Lithgow
Feb 16, 2020·Digestive Diseases and Sciences·Cade EmletRegina Lamendella
Sep 27, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Natalya Sh LebedevaOskar I Koifman
Dec 31, 2019·BMC Biology·F H CoutinhoF Rodríguez-Valera
Oct 6, 2020·Frontiers in Cellular and Infection Microbiology·Emma Guerin, Colin Hill
Jul 25, 2018·Archives of Virology·Peter Simmonds, Pakorn Aiewsakun
Dec 19, 2019·Frontiers in Endocrinology·Thomas D S Sutton, Colin Hill
Dec 13, 2019·PLoS Pathogens·Simon KäferChristian Drosten
Mar 7, 2020·Microbiology and Molecular Biology Reviews : MMBR·Eugene V KooninJens H Kuhn
Jun 27, 2020·Scientific Data·John C BramleyWilliam J Buchser
May 28, 2019·Viruses·Nikos VasilakisPeter J Walker
Oct 8, 2020·Archives of Virology·Adrian Gibbs
Mar 11, 2021·Periodontology 2000·Szymon P SzafrańskiMeike Stiesch
Apr 4, 2021·Viruses·Dann TurnerEvelien M Adriaenssens
Apr 22, 2021·BioDrugs : Clinical Immunotherapeutics, Biopharmaceuticals and Gene Therapy·Małgorzata ŁobockaAndrzej Górski
Sep 4, 2021·The ISME Journal·Nina BartlauCristina Moraru

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Datasets Mentioned

BETA
KX344510
MG065683

Methods Mentioned

BETA
electron-microscopy
protein profile

Software Mentioned

blastp
Genome Relationship Applied to Virus Taxonomy ; GRAViTy
vConTACT
GRAViTy

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