Phenetic Comparison of Prokaryotic Genomes Using k-mers
Identifieur interne : 000C34 ( Main/Exploration ); précédent : 000C33; suivant : 000C35Phenetic Comparison of Prokaryotic Genomes Using k-mers
Auteurs : Maxime Déraspe [Canada] ; Frédéric Raymond [Canada] ; Sébastien Boisvert [Canada] ; Alexander Culley [Canada] ; Paul H. Roy [Canada] ; François Laviolette [Canada] ; Jacques Corbeil [Canada]Source :
- Molecular Biology and Evolution [ 0737-4038 ] ; 2017.
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Abstract
Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of
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DOI: 10.1093/molbev/msx200
PubMed: 28957508
PubMed Central: 5850840
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Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC</wicri:regionArea><wicri:noRegion>QC</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="msx200-aff6">Département d’Informatique et de Génie Logiciel, Université Laval, Quebec City, QC, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Département d’Informatique et de Génie Logiciel, Université Laval, Quebec City, QC</wicri:regionArea><wicri:noRegion>QC</wicri:noRegion></affiliation></author><author><name sortKey="Corbeil, Jacques" sort="Corbeil, Jacques" uniqKey="Corbeil J" first="Jacques" last="Corbeil">Jacques Corbeil</name><affiliation wicri:level="1"><nlm:aff id="msx200-aff1">Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC</wicri:regionArea><wicri:noRegion>QC</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="msx200-aff2">Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC</wicri:regionArea><wicri:noRegion>QC</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="msx200-aff3">Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Département de Médecine Moléculaire, Université Laval, Quebec City, QC</wicri:regionArea><wicri:noRegion>QC</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular Biology and Evolution</title><idno type="ISSN">0737-4038</idno><idno type="eISSN">1537-1719</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (genetics)</term><term>Biological Evolution</term><term>Cluster Analysis</term><term>Computational Biology (methods)</term><term>Computer Simulation</term><term>Evolution, Molecular</term><term>Genome, Bacterial (genetics)</term><term>Genomics (methods)</term><term>Metagenomics</term><term>Phylogeny</term><term>Prokaryotic Cells</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN ()</term><term>Bactéries (génétique)</term><term>Biologie informatique ()</term><term>Cellules procaryotes</term><term>Génome bactérien (génétique)</term><term>Génomique ()</term><term>Logiciel</term><term>Métagénomique</term><term>Phylogénie</term><term>Simulation numérique</term><term>Évolution biologique</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term><term>Genome, Bacterial</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term><term>Génome bactérien</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Genomics</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biological Evolution</term><term>Cluster Analysis</term><term>Computer Simulation</term><term>Evolution, Molecular</term><term>Metagenomics</term><term>Phylogeny</term><term>Prokaryotic Cells</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Cellules procaryotes</term><term>Génomique</term><term>Logiciel</term><term>Métagénomique</term><term>Phylogénie</term><term>Simulation numérique</term><term>Évolution biologique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of <italic>Streptococcus pneumoniae</italic> and <italic>Pseudomonas aeruginosa</italic>. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in <italic>P. aeruginosa</italic> than in <italic>S. pneumoniae</italic>, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Allison, Ge" uniqKey="Allison G">GE Allison</name></author><author><name sortKey="Verma, Nk" uniqKey="Verma N">NK. 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Roy</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li></country></list><tree><country name="Canada"><noRegion><name sortKey="Deraspe, Maxime" sort="Deraspe, Maxime" uniqKey="Deraspe M" first="Maxime" last="Déraspe">Maxime Déraspe</name></noRegion><name sortKey="Boisvert, Sebastien" sort="Boisvert, Sebastien" uniqKey="Boisvert S" first="Sébastien" last="Boisvert">Sébastien Boisvert</name><name sortKey="Corbeil, Jacques" sort="Corbeil, Jacques" uniqKey="Corbeil J" first="Jacques" last="Corbeil">Jacques Corbeil</name><name sortKey="Corbeil, Jacques" sort="Corbeil, Jacques" uniqKey="Corbeil J" first="Jacques" last="Corbeil">Jacques Corbeil</name><name sortKey="Corbeil, Jacques" sort="Corbeil, Jacques" uniqKey="Corbeil J" first="Jacques" last="Corbeil">Jacques Corbeil</name><name sortKey="Culley, Alexander" sort="Culley, Alexander" uniqKey="Culley A" first="Alexander" last="Culley">Alexander Culley</name><name sortKey="Deraspe, Maxime" sort="Deraspe, Maxime" uniqKey="Deraspe M" first="Maxime" last="Déraspe">Maxime Déraspe</name><name sortKey="Deraspe, Maxime" sort="Deraspe, Maxime" uniqKey="Deraspe M" first="Maxime" last="Déraspe">Maxime Déraspe</name><name sortKey="Laviolette, Francois" sort="Laviolette, Francois" uniqKey="Laviolette F" first="François" last="Laviolette">François Laviolette</name><name sortKey="Laviolette, Francois" sort="Laviolette, Francois" uniqKey="Laviolette F" first="François" last="Laviolette">François Laviolette</name><name sortKey="Raymond, Frederic" sort="Raymond, Frederic" uniqKey="Raymond F" first="Frédéric" last="Raymond">Frédéric Raymond</name><name sortKey="Raymond, Frederic" sort="Raymond, Frederic" uniqKey="Raymond F" first="Frédéric" last="Raymond">Frédéric Raymond</name><name sortKey="Roy, Paul H" sort="Roy, Paul H" uniqKey="Roy P" first="Paul H." last="Roy">Paul H. 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