Alignment-free inference of hierarchical and reticulate phylogenomic relationships
Identifieur interne : 000E95 ( Main/Exploration ); précédent : 000E94; suivant : 000E96Alignment-free inference of hierarchical and reticulate phylogenomic relationships
Auteurs : Guillaume Bernard [Australie] ; Cheong Xin Chan [Australie] ; Yao-Ban Chan [Australie] ; Xin-Yi Chua [Australie] ; Yingnan Cong [Australie] ; James M. Hogan [Australie] ; Stefan R. Maetschke [Australie] ; Mark A. Ragan [Australie]Source :
- Briefings in Bioinformatics [ 1467-5463 ] ; 2017.
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Abstract
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA. Thus, next-generation phylogenomics must address computational scalability while rethinking the nature of orthogroups, the alignment of multiple sequences and the inference and comparison of trees. New phylogenomic workflows have begun to take shape based on so-called alignment-free (AF) approaches. Here, we review the conceptual foundations of AF phylogenetics for the hierarchical (vertical) and reticulate (lateral) components of genome evolution, focusing on methods based on
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DOI: 10.1093/bib/bbx067
PubMed: 28673025
PubMed Central: 6433738
Affiliations:
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Molecular Bioscience, St Lucia, Brisbane, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>University of Queensland, Institute for Molecular Bioscience, St Lucia, Brisbane, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Chan, Yao Ban" sort="Chan, Yao Ban" uniqKey="Chan Y" first="Yao-Ban" last="Chan">Yao-Ban Chan</name><affiliation wicri:level="4"><nlm:aff id="aff2">University of Melbourne, School of Mathematics and Statistics, Parkville, Melbourne, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>University of Melbourne, School of Mathematics and Statistics, Parkville, Melbourne, Victoria</wicri:regionArea><orgName type="university">Université de Melbourne</orgName><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></affiliation></author><author><name sortKey="Chua, Xin Yi" sort="Chua, Xin Yi" uniqKey="Chua X" first="Xin-Yi" last="Chua">Xin-Yi Chua</name><affiliation wicri:level="1"><nlm:aff id="aff3">QFAB Bioinformatics, Queensland Cyber Infrastructure Foundation Ltd, St Lucia, Brisbane, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>QFAB Bioinformatics, Queensland Cyber Infrastructure Foundation Ltd, St Lucia, Brisbane</wicri:regionArea><wicri:noRegion>Brisbane</wicri:noRegion></affiliation></author><author><name sortKey="Cong, Yingnan" sort="Cong, Yingnan" uniqKey="Cong Y" first="Yingnan" last="Cong">Yingnan Cong</name><affiliation wicri:level="1"><nlm:aff id="aff4">Institute for Molecular Bioscience, St Lucia Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Institute for Molecular Bioscience, St Lucia Queensland</wicri:regionArea><wicri:noRegion>St Lucia Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Hogan, James M" sort="Hogan, James M" uniqKey="Hogan J" first="James M" last="Hogan">James M. Hogan</name><affiliation wicri:level="1"><nlm:aff id="aff5">Queensland University of Technology, School of Electrical Engineering and Computer Science, Brisbane, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Queensland University of Technology, School of Electrical Engineering and Computer Science, Brisbane, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Maetschke, Stefan R" sort="Maetschke, Stefan R" uniqKey="Maetschke S" first="Stefan R" last="Maetschke">Stefan R. Maetschke</name><affiliation wicri:level="1"><nlm:aff id="aff6">IBM Research Australia, Carlton, Melbourne, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>IBM Research Australia, Carlton, Melbourne, Victoria</wicri:regionArea><wicri:noRegion>Victoria</wicri:noRegion></affiliation></author><author><name sortKey="Ragan, Mark A" sort="Ragan, Mark A" uniqKey="Ragan M" first="Mark A" last="Ragan">Mark A. Ragan</name><affiliation wicri:level="1"><nlm:aff id="aff7">University of Queensland, Institute for Molecular Bioscience, St Lucia, Brisbane, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>University of Queensland, Institute for Molecular Bioscience, St Lucia, Brisbane</wicri:regionArea><wicri:noRegion>Brisbane</wicri:noRegion></affiliation></author></analytic><series><title level="j">Briefings in Bioinformatics</title><idno type="ISSN">1467-5463</idno><idno type="eISSN">1477-4054</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Evolution, Molecular</term><term>Genome</term><term>Humans</term><term>Microbiota (genetics)</term><term>Models, Genetic</term><term>Phylogeny</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term><term>Viruses (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Génome</term><term>Humains</term><term>Microbiote (génétique)</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Virus (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microbiota</term><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Microbiote</term><term>Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Evolution, Molecular</term><term>Genome</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Génome</term><term>Humains</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA. Thus, next-generation phylogenomics must address computational scalability while rethinking the nature of orthogroups, the alignment of multiple sequences and the inference and comparison of trees. New phylogenomic workflows have begun to take shape based on so-called alignment-free (AF) approaches. Here, we review the conceptual foundations of AF phylogenetics for the hierarchical (vertical) and reticulate (lateral) components of genome evolution, focusing on methods based on <italic>k</italic>-mers. We reflect on what seems to be successful, and on where further development is needed.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Delsuc, F" uniqKey="Delsuc F">F Delsuc</name></author><author><name sortKey="Brinkmann, H" uniqKey="Brinkmann H">H Brinkmann</name></author><author><name sortKey="Philippe, H" uniqKey="Philippe H">H. Philippe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eisen, Ja" uniqKey="Eisen J">JA Eisen</name></author><author><name sortKey="Fraser, Cm" uniqKey="Fraser C">CM. 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Doolittle</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li></country><region><li>Victoria (État)</li></region><settlement><li>Melbourne</li></settlement><orgName><li>Université de Melbourne</li></orgName></list><tree><country name="Australie"><noRegion><name sortKey="Bernard, Guillaume" sort="Bernard, Guillaume" uniqKey="Bernard G" first="Guillaume" last="Bernard">Guillaume Bernard</name></noRegion><name sortKey="Chan, Cheong Xin" sort="Chan, Cheong Xin" uniqKey="Chan C" first="Cheong Xin" last="Chan">Cheong Xin Chan</name><name sortKey="Chan, Yao Ban" sort="Chan, Yao Ban" uniqKey="Chan Y" first="Yao-Ban" last="Chan">Yao-Ban Chan</name><name sortKey="Chua, Xin Yi" sort="Chua, Xin Yi" uniqKey="Chua X" first="Xin-Yi" last="Chua">Xin-Yi Chua</name><name sortKey="Cong, Yingnan" sort="Cong, Yingnan" uniqKey="Cong Y" first="Yingnan" last="Cong">Yingnan Cong</name><name sortKey="Hogan, James M" sort="Hogan, James M" uniqKey="Hogan J" first="James M" last="Hogan">James M. Hogan</name><name sortKey="Maetschke, Stefan R" sort="Maetschke, Stefan R" uniqKey="Maetschke S" first="Stefan R" last="Maetschke">Stefan R. Maetschke</name><name sortKey="Ragan, Mark A" sort="Ragan, Mark A" uniqKey="Ragan M" first="Mark A" last="Ragan">Mark A. Ragan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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