VirClust—A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of (Prokaryotic) Viruses

Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of viruses”, recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are c...

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Vydáno v:	Viruses Ročník 15; číslo 4; s. 1007
Hlavní autor:	Moraru, Cristina
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Switzerland MDPI AG 19.04.2023 MDPI
Témata:	bacteriophages Bacteriophages - genetics Classification Cluster Analysis Core protein data collection Genes Genes, Viral Genome, Viral Genomes Identification and classification Markov chains phage classification Phylogenetics Phylogeny Physiological aspects protein content Proteins Taxonomy viral genome Viral proteins VirClust virus classification virus genome clustering virus protein annotation virus protein clustering Viruses Viruses - genetics Germany United States > US VirClust shared viral proteins core proteins phage classification virus classification virus protein clustering virus genome clustering virus protein annotation
ISSN:	1999-4915, 1999-4915
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Abstract	Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of viruses”, recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are classified into hierarchical taxons, ideally defined by the phylogeny of their shared genes. To enable the detection of shared genes, viruses have first to be clustered, and there is currently a need for tools to assist with virus clustering and classification. Here, VirClust is presented. It is a novel, reference-free tool capable of performing: (i) protein clustering, based on BLASTp and Hidden Markov Models (HMMs) similarities; (ii) hierarchical clustering of viruses based on intergenomic distances calculated from their shared protein content; (iii) identification of core proteins and (iv) annotation of viral proteins. VirClust has flexible parameters both for protein clustering and for splitting the viral genome tree into smaller genome clusters, corresponding to different taxonomic levels. Benchmarking on a phage dataset showed that the genome trees produced by VirClust match the current ICTV classification at family, sub-family and genus levels. VirClust is freely available, as a web-service and stand-alone tool.
AbstractList	Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called "megataxonomy of viruses", recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are classified into hierarchical taxons, ideally defined by the phylogeny of their shared genes. To enable the detection of shared genes, viruses have first to be clustered, and there is currently a need for tools to assist with virus clustering and classification. Here, VirClust is presented. It is a novel, reference-free tool capable of performing: (i) protein clustering, based on BLASTp and Hidden Markov Models (HMMs) similarities; (ii) hierarchical clustering of viruses based on intergenomic distances calculated from their shared protein content; (iii) identification of core proteins and (iv) annotation of viral proteins. VirClust has flexible parameters both for protein clustering and for splitting the viral genome tree into smaller genome clusters, corresponding to different taxonomic levels. Benchmarking on a phage dataset showed that the genome trees produced by VirClust match the current ICTV classification at family, sub-family and genus levels. VirClust is freely available, as a web-service and stand-alone tool. Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called "megataxonomy of viruses", recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are classified into hierarchical taxons, ideally defined by the phylogeny of their shared genes. To enable the detection of shared genes, viruses have first to be clustered, and there is currently a need for tools to assist with virus clustering and classification. Here, VirClust is presented. It is a novel, reference-free tool capable of performing: (i) protein clustering, based on BLASTp and Hidden Markov Models (HMMs) similarities; (ii) hierarchical clustering of viruses based on intergenomic distances calculated from their shared protein content; (iii) identification of core proteins and (iv) annotation of viral proteins. VirClust has flexible parameters both for protein clustering and for splitting the viral genome tree into smaller genome clusters, corresponding to different taxonomic levels. Benchmarking on a phage dataset showed that the genome trees produced by VirClust match the current ICTV classification at family, sub-family and genus levels. VirClust is freely available, as a web-service and stand-alone tool.Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called "megataxonomy of viruses", recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are classified into hierarchical taxons, ideally defined by the phylogeny of their shared genes. To enable the detection of shared genes, viruses have first to be clustered, and there is currently a need for tools to assist with virus clustering and classification. Here, VirClust is presented. It is a novel, reference-free tool capable of performing: (i) protein clustering, based on BLASTp and Hidden Markov Models (HMMs) similarities; (ii) hierarchical clustering of viruses based on intergenomic distances calculated from their shared protein content; (iii) identification of core proteins and (iv) annotation of viral proteins. VirClust has flexible parameters both for protein clustering and for splitting the viral genome tree into smaller genome clusters, corresponding to different taxonomic levels. Benchmarking on a phage dataset showed that the genome trees produced by VirClust match the current ICTV classification at family, sub-family and genus levels. VirClust is freely available, as a web-service and stand-alone tool.
Audience	Academic
Author	Moraru, Cristina
AuthorAffiliation	Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky–Str. 9-11, 26111 Oldenburg, Germany; liliana.cristina.moraru@uni-oldenburg.de
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/37112988$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1093/nar/30.7.1575 10.1101/2020.07.05.188268 10.1186/s12859-019-3019-7 10.1093/nar/gkw1107 10.1128/JVI.00673-21 10.1007/978-3-540-35306-5 10.1038/s41579-019-0205-6 10.1093/bioinformatics/btl117 10.7717/peerj.985 10.1186/s40168-018-0422-7 10.1038/s41587-019-0100-8 10.1371/journal.pbio.3001922 10.1038/s41467-019-11433-0 10.1093/bioinformatics/btw313 10.7717/peerj.3243 10.1038/nmeth.1818 10.1128/MMBR.00061-19 10.1093/bioinformatics/btu031 10.1073/pnas.1621061114 10.1093/nargab/lqab067 10.1093/ve/veac070 10.1093/bioinformatics/btx440 10.1093/bioinformatics/btx157 10.1093/nar/gkab301 10.1002/pro.3290 10.1186/1471-2105-14-120 10.3390/v11050401 10.1093/bioinformatics/btab451 10.1186/1471-2105-10-421 10.1099/jgv.0.001110 10.3389/fevo.2019.00174 10.1371/journal.pcbi.1002195 10.1128/mBio.00978-16 10.1186/1745-6150-1-29 10.1038/s41564-020-0709-x 10.1093/nar/gkw975
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References	(ref_13) 2017; 33 Letunic (ref_35) 2021; 49 ref_11 Suzuki (ref_24) 2006; 22 ref_10 ref_32 Krupovic (ref_6) 2019; 17 Kazlauskas (ref_7) 2019; 10 Aiewsakun (ref_15) 2018; 99 ref_31 Noguchi (ref_19) 2008; 15 Iranzo (ref_8) 2016; 7 Koonin (ref_1) 2020; 84 ref_18 Aiewsakun (ref_14) 2018; 6 Jones (ref_34) 2014; 30 Grazziotin (ref_28) 2017; 45 Zayed (ref_38) 2021; 37 Bolduc (ref_17) 2019; 37 Bolduc (ref_16) 2017; 5 Krupovic (ref_5) 2017; 114 Koonin (ref_4) 2006; 1 Terzian (ref_30) 2021; 3 Krupovic (ref_9) 2021; 95 ref_21 Nishimura (ref_12) 2017; 33 ref_20 Gu (ref_27) 2016; 32 ref_40 Zucker (ref_36) 2022; 8 ref_3 Remmert (ref_23) 2011; 9 Shimodaira (ref_25) 2019; 7 ref_29 Enright (ref_39) 2002; 30 Gorbalenya (ref_2) 2020; 5 ref_26 Finn (ref_33) 2017; 45 Sievers (ref_22) 2018; 27 Roux (ref_37) 2015; 3
References_xml	– volume: 30 start-page: 1575 year: 2002 ident: ref_39 article-title: An efficient algorithm for large-scale detection of protein families publication-title: Nucleic Acids Res. doi: 10.1093/nar/30.7.1575 – ident: ref_11 doi: 10.1101/2020.07.05.188268 – ident: ref_31 doi: 10.1186/s12859-019-3019-7 – volume: 45 start-page: D190 year: 2017 ident: ref_33 article-title: InterPro in 2017-beyond protein family and domain annotations publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw1107 – volume: 95 start-page: e00673-21 year: 2021 ident: ref_9 article-title: Adnaviria: A new realm for archaeal filamentous viruses with linear A-form double-stranded DNA genomes publication-title: J. Virol. doi: 10.1128/JVI.00673-21 – ident: ref_20 doi: 10.1007/978-3-540-35306-5 – ident: ref_26 – volume: 17 start-page: 449 year: 2019 ident: ref_6 article-title: Origin of viruses: Primordial replicators recruiting capsids from hosts publication-title: Nat. Rev. Microbiol. doi: 10.1038/s41579-019-0205-6 – volume: 22 start-page: 1540 year: 2006 ident: ref_24 article-title: Pvclust: An R package for assessing the uncertainty in hierarchical clustering publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl117 – volume: 3 start-page: e985 year: 2015 ident: ref_37 article-title: VirSorter: Mining viral signal from microbial genomic data publication-title: PeerJ doi: 10.7717/peerj.985 – volume: 6 start-page: 38 year: 2018 ident: ref_14 article-title: The genomic underpinnings of eukaryotic virus taxonomy: Creating a sequence-based framework for family-level virus classification publication-title: Microbiome doi: 10.1186/s40168-018-0422-7 – volume: 37 start-page: 632 year: 2019 ident: ref_17 article-title: Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks publication-title: Nat. Biotechnol. doi: 10.1038/s41587-019-0100-8 – ident: ref_3 doi: 10.1371/journal.pbio.3001922 – volume: 10 start-page: 3425 year: 2019 ident: ref_7 article-title: Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids publication-title: Nat. Commun. doi: 10.1038/s41467-019-11433-0 – volume: 32 start-page: 2847 year: 2016 ident: ref_27 article-title: Complex heatmaps reveal patterns and correlations in multidimensional genomic data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw313 – ident: ref_18 – volume: 15 start-page: 387 year: 2008 ident: ref_19 article-title: MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes publication-title: DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes – volume: 5 start-page: e3243 year: 2017 ident: ref_16 article-title: vConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria publication-title: PeerJ doi: 10.7717/peerj.3243 – volume: 9 start-page: 173 year: 2011 ident: ref_23 article-title: HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment publication-title: Nat. Methods doi: 10.1038/nmeth.1818 – volume: 84 start-page: e00061-19 year: 2020 ident: ref_1 article-title: Global Organization and Proposed Megataxonomy of the Virus World publication-title: Microbiol. Mol. Biol. Rev. doi: 10.1128/MMBR.00061-19 – volume: 30 start-page: 1236 year: 2014 ident: ref_34 article-title: InterProScan 5: Genome-scale protein function classification publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu031 – volume: 114 start-page: E2401 year: 2017 ident: ref_5 article-title: Multiple origins of viral capsid proteins from cellular ancestors publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1621061114 – volume: 3 start-page: lqab067 year: 2021 ident: ref_30 article-title: PHROG: Families of prokaryotic virus proteins clustered using remote homology publication-title: NAR Genom. Bioinform. doi: 10.1093/nargab/lqab067 – volume: 8 start-page: veac070 year: 2022 ident: ref_36 article-title: New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria publication-title: Virus Evol. doi: 10.1093/ve/veac070 – volume: 33 start-page: 3396 year: 2017 ident: ref_13 article-title: VICTOR: Genome-based phylogeny and classification of prokaryotic viruses publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx440 – volume: 33 start-page: 2379 year: 2017 ident: ref_12 article-title: ViPTree: The viral proteomic tree server publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx157 – ident: ref_10 – volume: 49 start-page: W293 year: 2021 ident: ref_35 article-title: Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkab301 – volume: 27 start-page: 135 year: 2018 ident: ref_22 article-title: Clustal Omega for making accurate alignments of many protein sequences publication-title: Protein Sci. doi: 10.1002/pro.3290 – ident: ref_40 doi: 10.1186/1471-2105-14-120 – ident: ref_29 doi: 10.3390/v11050401 – volume: 37 start-page: 4202 year: 2021 ident: ref_38 article-title: efam: An expanded, metaproteome-supported HMM profile database of viral protein families publication-title: Bioinformatics doi: 10.1093/bioinformatics/btab451 – ident: ref_21 doi: 10.1186/1471-2105-10-421 – volume: 99 start-page: 1331 year: 2018 ident: ref_15 article-title: Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: Steps towards a unified taxonomy publication-title: J. Gen. Virol. doi: 10.1099/jgv.0.001110 – volume: 7 start-page: 459 year: 2019 ident: ref_25 article-title: Selective Inference for Testing Trees and Edges in Phylogenetics publication-title: Front. Ecol. Evol. doi: 10.3389/fevo.2019.00174 – ident: ref_32 doi: 10.1371/journal.pcbi.1002195 – volume: 7 start-page: e00978-16 year: 2016 ident: ref_8 article-title: The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing publication-title: mBio doi: 10.1128/mBio.00978-16 – volume: 1 start-page: 29 year: 2006 ident: ref_4 article-title: The ancient Virus World and evolution of cells publication-title: Biol. Direct doi: 10.1186/1745-6150-1-29 – volume: 5 start-page: 668 year: 2020 ident: ref_2 article-title: The new scope of virus taxonomy: Partitioning the virosphere into 15 hierarchical ranks publication-title: Nat. Microbiol. doi: 10.1038/s41564-020-0709-x – volume: 45 start-page: D491 year: 2017 ident: ref_28 article-title: Prokaryotic virus orthologous groups (pVOGs): A resource for comparative genomics and protein family annotation publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw975
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Snippet	Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of... Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called "megataxonomy of...
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SubjectTerms	bacteriophages Bacteriophages - genetics Classification Cluster Analysis Core protein data collection Genes Genes, Viral Genome, Viral Genomes Identification and classification Markov chains phage classification Phylogenetics Phylogeny Physiological aspects protein content Proteins Taxonomy viral genome Viral proteins VirClust virus classification virus genome clustering virus protein annotation virus protein clustering Viruses Viruses - genetics
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Title	VirClust—A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of (Prokaryotic) Viruses
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