Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer
Identifieur interne : 001919 ( Ncbi/Curation ); précédent : 001918; suivant : 001920Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer
Auteurs : Qian Zhang [États-Unis] ; Se-Ran Jun [États-Unis] ; Michael Leuze [États-Unis] ; David Ussery [États-Unis] ; Intawat Nookaew [États-Unis]Source :
- Scientific Reports [ 2045-2322 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Virus.
- Bases de données génétiques, Biologie informatique, Génome viral, Génomique, Phylogénie, Taille du génome, Virus.
English descriptors
- KwdEn :
- MESH :
- classification : Viruses.
- genetics : Viruses.
- methods : Genomics.
- Computational Biology, Databases, Genetic, Genome Size, Genome, Viral, Phylogeny, Whole Genome Sequencing.
Abstract
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral “tree of life”. However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses
The online version of this article (doi:10.1038/srep40712) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1038/srep40712
PubMed: 28102365
PubMed Central: 5244389
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sortKey="Zhang, Qian" sort="Zhang, Qian" uniqKey="Zhang Q" first="Qian" last="Zhang">Qian Zhang</name><affiliation wicri:level="2"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.411461.7</institution-id><institution-id institution-id-type="ISNI">0000 0001 2315 1184</institution-id><institution>UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee,</institution></institution-wrap>Knoxville, TN 37996 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Knoxville</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff2">Biosciences Division, Comparative Genomics Group, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Biosciences Division, Comparative Genomics Group, Oak Ridge National 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Rock</wicri:cityArea></affiliation></author><author><name sortKey="Leuze, Michael" sort="Leuze, Michael" uniqKey="Leuze M" first="Michael" last="Leuze">Michael Leuze</name><affiliation wicri:level="2"><nlm:aff id="Aff4"><institution-wrap><institution-id institution-id-type="GRID">grid.503033.6</institution-id><institution>Joint Institute for Computational Sciences, University of Tennessee,</institution></institution-wrap>Knoxville, TN 37831 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Knoxville</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff5">Computer Science and Mathematics Division, Computational Biomolecular Modeling and Bioinformatics Group, Oak Ridge National Laboratories, Oak Ridge, TN 37831 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Computer Science and Mathematics Division, Computational Biomolecular Modeling and Bioinformatics Group, Oak Ridge National Laboratories, Oak Ridge</wicri:cityArea></affiliation></author><author><name sortKey="Ussery, David" sort="Ussery, David" uniqKey="Ussery D" first="David" last="Ussery">David Ussery</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Biosciences Division, Comparative Genomics Group, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Biosciences Division, Comparative Genomics Group, Oak Ridge National Laboratory Oak Ridge</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arkansas</region></placeName><wicri:cityArea>Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock</wicri:cityArea></affiliation></author><author><name sortKey="Nookaew, Intawat" sort="Nookaew, Intawat" uniqKey="Nookaew I" first="Intawat" last="Nookaew">Intawat Nookaew</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Biosciences Division, Comparative Genomics Group, Oak Ridge National Laboratory Oak Ridge, TN 37831 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Tennessee</region></placeName><wicri:cityArea>Biosciences Division, Comparative Genomics Group, Oak Ridge National Laboratory Oak Ridge</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arkansas</region></placeName><wicri:cityArea>Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock</wicri:cityArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology</term><term>Databases, Genetic</term><term>Genome Size</term><term>Genome, Viral</term><term>Genomics (methods)</term><term>Phylogeny</term><term>Viruses (classification)</term><term>Viruses (genetics)</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Génome viral</term><term>Génomique ()</term><term>Phylogénie</term><term>Taille du génome</term><term>Virus ()</term><term>Virus (génétique)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Databases, Genetic</term><term>Genome Size</term><term>Genome, Viral</term><term>Phylogeny</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Génome viral</term><term>Génomique</term><term>Phylogénie</term><term>Taille du génome</term><term>Virus</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="Par1">The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral “tree of life”. However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses <italic>k</italic>-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, <italic>k</italic> (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine <italic>k</italic> for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.</p><sec><title>Supplementary information</title><p>The online version of this article (doi:10.1038/srep40712) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Royer Bertrand, B" uniqKey="Royer Bertrand B">B Royer-Bertrand</name></author><author><name sortKey="Rivolta, C" uniqKey="Rivolta C">C Rivolta</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schlotterer, C" uniqKey="Schlotterer C">C Schlötterer</name></author><author><name sortKey="Tobler, R" uniqKey="Tobler R">R Tobler</name></author><author><name sortKey="Kofler, R" uniqKey="Kofler R">R Kofler</name></author><author><name sortKey="Nolte, V" uniqKey="Nolte V">V Nolte</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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sortKey="Huang, Hh" uniqKey="Huang H">HH Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, Hh" uniqKey="Huang H">HH Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Labonte, Jm" uniqKey="Labonte J">JM Labonté</name></author><author><name sortKey="Suttle, Ca" uniqKey="Suttle C">CA Suttle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Furuse, Y" uniqKey="Furuse Y">Y Furuse</name></author><author><name sortKey="Suzuki, A" uniqKey="Suzuki A">A Suzuki</name></author><author><name sortKey="Kamigaki, T" uniqKey="Kamigaki T">T Kamigaki</name></author><author><name sortKey="Oshitani, H" uniqKey="Oshitani H">H Oshitani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shi, W" uniqKey="Shi W">W Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tatusova, T" uniqKey="Tatusova T">T Tatusova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jun, S R" uniqKey="Jun S">S-R Jun</name></author><author><name sortKey="Sims, Ge" uniqKey="Sims G">GE Sims</name></author><author><name sortKey="Wu, Ga" uniqKey="Wu G">GA Wu</name></author><author><name sortKey="Kim, S H" uniqKey="Kim S">S-H Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jun, Sr" uniqKey="Jun S">SR Jun</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Varghese, Nj" uniqKey="Varghese N">NJ Varghese</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marçais</name></author><author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Revell, Lj" uniqKey="Revell L">LJ Revell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sadovsky, Mg" uniqKey="Sadovsky M">MG Sadovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kullback, S" uniqKey="Kullback S">S Kullback</name></author><author><name sortKey="Leibler, Ra" uniqKey="Leibler R">RA Leibler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shannon, Ce" uniqKey="Shannon C">CE Shannon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Robinson, Df" uniqKey="Robinson D">DF Robinson</name></author><author><name sortKey="Foulds, Lr" uniqKey="Foulds L">LR Foulds</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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