Phenetic Comparison of Prokaryotic Genomes Using k-mers
Identifieur interne : 000747 ( Pmc/Checkpoint ); précédent : 000746; suivant : 000748Phenetic 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.
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
Url:
DOI: 10.1093/molbev/msx200
PubMed: 28957508
PubMed Central: 5850840
Affiliations:
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<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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Mol Biol Evol</journal-id>
<journal-id journal-id-type="iso-abbrev">Mol. Biol. Evol</journal-id>
<journal-id journal-id-type="publisher-id">molbev</journal-id>
<journal-title-group><journal-title>Molecular Biology and Evolution</journal-title>
</journal-title-group>
<issn pub-type="ppub">0737-4038</issn>
<issn pub-type="epub">1537-1719</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">28957508</article-id>
<article-id pub-id-type="pmc">5850840</article-id>
<article-id pub-id-type="doi">10.1093/molbev/msx200</article-id>
<article-id pub-id-type="publisher-id">msx200</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Methods</subject>
</subj-group>
</article-categories>
<title-group><article-title>Phenetic Comparison of Prokaryotic Genomes Using k-mers</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Déraspe</surname>
<given-names>Maxime</given-names>
</name>
<xref ref-type="author-notes" rid="msx200-FM1"></xref>
<xref ref-type="aff" rid="msx200-aff1">1</xref>
<xref ref-type="aff" rid="msx200-aff2">2</xref>
<xref ref-type="aff" rid="msx200-aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Raymond</surname>
<given-names>Frédéric</given-names>
</name>
<xref ref-type="author-notes" rid="msx200-FM1"></xref>
<xref ref-type="aff" rid="msx200-aff1">1</xref>
<xref ref-type="aff" rid="msx200-aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Boisvert</surname>
<given-names>Sébastien</given-names>
</name>
<xref ref-type="aff" rid="msx200-aff4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Culley</surname>
<given-names>Alexander</given-names>
</name>
<xref ref-type="aff" rid="msx200-aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Roy</surname>
<given-names>Paul H.</given-names>
</name>
<xref ref-type="aff" rid="msx200-aff1">1</xref>
<xref ref-type="aff" rid="msx200-aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Laviolette</surname>
<given-names>François</given-names>
</name>
<xref ref-type="author-notes" rid="msx200-FM2"></xref>
<xref ref-type="aff" rid="msx200-aff2">2</xref>
<xref ref-type="aff" rid="msx200-aff6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Corbeil</surname>
<given-names>Jacques</given-names>
</name>
<xref ref-type="corresp" rid="msx200-cor1"></xref>
<pmc-comment>jacques.corbeil@genome.ulaval.ca </pmc-comment>
<xref ref-type="author-notes" rid="msx200-FM2"></xref>
<xref ref-type="aff" rid="msx200-aff1">1</xref>
<xref ref-type="aff" rid="msx200-aff2">2</xref>
<xref ref-type="aff" rid="msx200-aff3">3</xref>
</contrib>
</contrib-group>
<aff id="msx200-aff1"><label>1</label>
Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada</aff>
<aff id="msx200-aff2"><label>2</label>
Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada</aff>
<aff id="msx200-aff3"><label>3</label>
Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada</aff>
<aff id="msx200-aff4"><label>4</label>
Gydle Inc., Quebec City, QC, Canada</aff>
<aff id="msx200-aff5"><label>5</label>
Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Quebec City, QC, Canada</aff>
<aff id="msx200-aff6"><label>6</label>
Département d’Informatique et de Génie Logiciel, Université Laval, Quebec City, QC, Canada</aff>
<author-notes><fn id="msx200-FM1"><label>†</label>
<p>These authors contributed equally to this work.</p>
</fn>
<fn id="msx200-FM2"><label>‡</label>
<p>Shared senior authorship.</p>
</fn>
<corresp id="msx200-cor1"><label>*</label>
<bold>Corresponding author:</bold>
E-mail: <email>jacques.corbeil@genome.ulaval.ca</email>
.</corresp>
<fn id="msx200-FM3"><p><bold>Associate editor:</bold>
Miriam Barlow</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>10</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="epub" iso-8601-date="2017-07-16"><day>16</day>
<month>7</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>16</day>
<month>7</month>
<year>2017</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the . </pmc-comment>
<volume>34</volume>
<issue>10</issue>
<fpage>2716</fpage>
<lpage>2729</lpage>
<permissions><copyright-statement>© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</copyright-statement>
<copyright-year>2017</copyright-year>
<license license-type="cc-by-nc" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>
), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p>
</license>
</permissions>
<self-uri xlink:href="msx200.pdf"></self-uri>
<abstract><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>
</abstract>
<kwd-group kwd-group-type="author"><kwd>comparative genomics</kwd>
<kwd>microbial evolution</kwd>
<kwd>population structure</kwd>
<kwd>horizontal gene transfer</kwd>
<kwd>software</kwd>
</kwd-group>
<counts><page-count count="14"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<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. Roy</name>
<name sortKey="Roy, Paul H" sort="Roy, Paul H" uniqKey="Roy P" first="Paul H." last="Roy">Paul H. Roy</name>
</country>
</tree>
</affiliations>
</record>
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