Alignment-free inference of hierarchical and reticulate phylogenomic relationships.
Identifieur interne : 000C37 ( PubMed/Curation ); précédent : 000C36; suivant : 000C38Alignment-free inference of hierarchical and reticulate phylogenomic relationships.
Auteurs : Guillaume Bernard ; Cheong Xin Chan ; Yao-Ban Chan ; Xin-Yi Chua ; Yingnan Cong ; James M. Hogan ; Stefan R. Maetschke ; Mark A. RaganSource :
- Briefings in bioinformatics [ 1477-4054 ] ; 2019.
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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 k-mers. We reflect on what seems to be successful, and on where further development is needed.
DOI: 10.1093/bib/bbx067
PubMed: 28673025
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Guillaume Bernard<affiliation><nlm:affiliation>Institute for Molecular Bioscience.</nlm:affiliation><wicri:noCountry code="no comma">Institute for Molecular Bioscience.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>University of Queensland.</nlm:affiliation><wicri:noCountry code="no comma">University of Queensland.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>University of Melbourne.</nlm:affiliation><wicri:noCountry code="no comma">University of Melbourne.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>QFAB Bioinformatics.</nlm:affiliation><wicri:noCountry code="no comma">QFAB Bioinformatics.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>University of Queensland.</nlm:affiliation><wicri:noCountry code="no comma">University of Queensland.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Queensland University of Technology.</nlm:affiliation><wicri:noCountry code="no comma">Queensland University of Technology.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>IBM Research Australia.</nlm:affiliation><wicri:noCountry code="no comma">IBM Research Australia.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Institute for Molecular Bioscience.</nlm:affiliation><wicri:noCountry code="no comma">Institute for Molecular Bioscience.</wicri:noCountry></affiliation>Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Alignment-free inference of hierarchical and reticulate phylogenomic relationships.</title><author><name sortKey="Bernard, Guillaume" sort="Bernard, Guillaume" uniqKey="Bernard G" first="Guillaume" last="Bernard">Guillaume Bernard</name><affiliation><nlm:affiliation>Institute for Molecular Bioscience.</nlm:affiliation><wicri:noCountry code="no comma">Institute for Molecular Bioscience.</wicri:noCountry></affiliation></author><author><name sortKey="Chan, Cheong Xin" sort="Chan, Cheong Xin" uniqKey="Chan C" first="Cheong Xin" last="Chan">Cheong Xin Chan</name><affiliation><nlm:affiliation>University of Queensland.</nlm:affiliation><wicri:noCountry code="no comma">University of Queensland.</wicri:noCountry></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><nlm:affiliation>University of Melbourne.</nlm:affiliation><wicri:noCountry code="no comma">University of Melbourne.</wicri:noCountry></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><nlm:affiliation>QFAB Bioinformatics.</nlm:affiliation><wicri:noCountry code="no comma">QFAB Bioinformatics.</wicri:noCountry></affiliation></author><author><name sortKey="Cong, Yingnan" sort="Cong, Yingnan" uniqKey="Cong Y" first="Yingnan" last="Cong">Yingnan Cong</name><affiliation><nlm:affiliation>University of Queensland.</nlm:affiliation><wicri:noCountry code="no comma">University of Queensland.</wicri:noCountry></affiliation></author><author><name sortKey="Hogan, James M" sort="Hogan, James M" uniqKey="Hogan J" first="James M" last="Hogan">James M. 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Ragan</name><affiliation><nlm:affiliation>Institute for Molecular Bioscience.</nlm:affiliation><wicri:noCountry code="no comma">Institute for Molecular Bioscience.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Briefings in bioinformatics</title><idno type="eISSN">1477-4054</idno><imprint><date when="2019" type="published">2019</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">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 k-mers. We reflect on what seems to be successful, and on where further development is needed.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28673025</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>04</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>06</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1477-4054</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>2</Issue><PubDate><Year>2019</Year><Month>03</Month><Day>22</Day></PubDate></JournalIssue><Title>Briefings in bioinformatics</Title><ISOAbbreviation>Brief. Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Alignment-free inference of hierarchical and reticulate phylogenomic relationships.</ArticleTitle><Pagination><MedlinePgn>426-435</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bib/bbx067</ELocationID><Abstract><AbstractText>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 k-mers. We reflect on what seems to be successful, and on where further development is needed.</AbstractText><CopyrightInformation>© The Author 2017. Published by Oxford University Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bernard</LastName><ForeName>Guillaume</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Institute for Molecular Bioscience.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chan</LastName><ForeName>Cheong Xin</ForeName><Initials>CX</Initials><AffiliationInfo><Affiliation>University of Queensland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chan</LastName><ForeName>Yao-Ban</ForeName><Initials>YB</Initials><AffiliationInfo><Affiliation>University of Melbourne.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chua</LastName><ForeName>Xin-Yi</ForeName><Initials>XY</Initials><AffiliationInfo><Affiliation>QFAB Bioinformatics.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cong</LastName><ForeName>Yingnan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>University of Queensland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hogan</LastName><ForeName>James M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Queensland University of Technology.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Maetschke</LastName><ForeName>Stefan R</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>IBM Research Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ragan</LastName><ForeName>Mark A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Institute for Molecular Bioscience.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., 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