k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank
Identifieur interne : 000A97 ( Main/Exploration ); précédent : 000A96; suivant : 000A98k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank
Auteurs : Guillaume Bernard [Australie] ; Paul Greenfield [Australie] ; Mark A. Ragan [Australie] ; Cheong Xin Chan [Australie]Source :
- mSystems [ 2379-5077 ] ; 2018.
Abstract
Genome evolution of microbes involves parent-to-offspring descent, and lateral genetic transfer that convolutes the phylogenomic signal. This study investigated phylogenomic signals among thousands of microbial genomes based on short subsequences without using multiple-sequence alignment. The signal from ribosomal RNAs is strong across all taxa, and the signal of plasmids is strong only in closely related groups, particularly
Url:
DOI: 10.1128/mSystems.00257-18
PubMed: 30505941
PubMed Central: 6247013
Affiliations:
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Ragan</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD</wicri:regionArea><wicri:noRegion>QLD</wicri:noRegion></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 wicri:level="1"><nlm:aff id="aff1"><addr-line>Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD</wicri:regionArea><wicri:noRegion>QLD</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD</wicri:regionArea><wicri:noRegion>QLD</wicri:noRegion></affiliation></author></analytic><series><title level="j">mSystems</title><idno type="eISSN">2379-5077</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Genome evolution of microbes involves parent-to-offspring descent, and lateral genetic transfer that convolutes the phylogenomic signal. This study investigated phylogenomic signals among thousands of microbial genomes based on short subsequences without using multiple-sequence alignment. The signal from ribosomal RNAs is strong across all taxa, and the signal of plasmids is strong only in closely related groups, particularly <italic>Proteobacteria</italic>. However, the signal from other chromosomal regions (∼99% of the genomes) is remarkably restricted in breadth. The similarity of subsequences is found to correlate with taxonomic rank and informs on conserved and differential core functions relative to niche specialization and evolutionary diversification of microbes. 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sortKey="Chan, Cheong Xin" sort="Chan, Cheong Xin" uniqKey="Chan C" first="Cheong Xin" last="Chan">Cheong Xin Chan</name><name sortKey="Chan, Cheong Xin" sort="Chan, Cheong Xin" uniqKey="Chan C" first="Cheong Xin" last="Chan">Cheong Xin Chan</name><name sortKey="Greenfield, Paul" sort="Greenfield, Paul" uniqKey="Greenfield P" first="Paul" last="Greenfield">Paul Greenfield</name><name sortKey="Ragan, Mark A" sort="Ragan, Mark A" uniqKey="Ragan M" first="Mark A." last="Ragan">Mark A. 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