Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy
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...
| Main Authors: | , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
Microbiology Society
2018
|
| _version_ | 1826275598078574592 |
|---|---|
| author | Aiewsakun, P Adriaenssens, E Lavigne, R Kropinski, A Simmonds, P |
| author_facet | Aiewsakun, P Adriaenssens, E Lavigne, R Kropinski, A Simmonds, P |
| author_sort | Aiewsakun, P |
| collection | OXFORD |
| description | 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 (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of eukaryotic viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1virus taxa as new virus families. The current study applied a common benchmark with which to compare taxonomies of eukaryotic and prokaryotic viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of viruses into which the vast body of metagenomic viral sequences may be consistently assigned. |
| first_indexed | 2024-03-06T23:01:11Z |
| format | Journal article |
| id | oxford-uuid:622ebbfa-2388-4c31-8126-26225f46a4d3 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T23:01:11Z |
| publishDate | 2018 |
| publisher | Microbiology Society |
| record_format | dspace |
| spelling | oxford-uuid:622ebbfa-2388-4c31-8126-26225f46a4d32022-03-26T18:04:33ZEvaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomyJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:622ebbfa-2388-4c31-8126-26225f46a4d3EnglishSymplectic Elements at OxfordMicrobiology Society2018Aiewsakun, PAdriaenssens, ELavigne, RKropinski, ASimmonds, PGenome 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 (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of eukaryotic viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1virus taxa as new virus families. The current study applied a common benchmark with which to compare taxonomies of eukaryotic and prokaryotic viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of viruses into which the vast body of metagenomic viral sequences may be consistently assigned. |
| spellingShingle | Aiewsakun, P Adriaenssens, E Lavigne, R Kropinski, A Simmonds, P Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy |
| title | Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy |
| title_full | Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy |
| title_fullStr | Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy |
| title_full_unstemmed | Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy |
| title_short | Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy |
| title_sort | evaluation of the genomic diversity of viruses infecting bacteria archaea and eukaryotes using a common bioinformatic platform steps towards a unified taxonomy |
| work_keys_str_mv | AT aiewsakunp evaluationofthegenomicdiversityofvirusesinfectingbacteriaarchaeaandeukaryotesusingacommonbioinformaticplatformstepstowardsaunifiedtaxonomy AT adriaenssense evaluationofthegenomicdiversityofvirusesinfectingbacteriaarchaeaandeukaryotesusingacommonbioinformaticplatformstepstowardsaunifiedtaxonomy AT lavigner evaluationofthegenomicdiversityofvirusesinfectingbacteriaarchaeaandeukaryotesusingacommonbioinformaticplatformstepstowardsaunifiedtaxonomy AT kropinskia evaluationofthegenomicdiversityofvirusesinfectingbacteriaarchaeaandeukaryotesusingacommonbioinformaticplatformstepstowardsaunifiedtaxonomy AT simmondsp evaluationofthegenomicdiversityofvirusesinfectingbacteriaarchaeaandeukaryotesusingacommonbioinformaticplatformstepstowardsaunifiedtaxonomy |