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Article: Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus

TitlePhylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus
Authors
KeywordsStreptococcus sinensis
Genome
Phylogenomic
“Sinensis group”
Illumina
Issue Date2014
PublisherOxford University Press for Society for Molecular Biology and Evolution. The Journal's web site is located at http://gbe.oxfordjournals.org
Citation
Genome Biology and Evolution, 2014, v. 6 n. 10, p. 2930-2943 How to Cite?
AbstractStreptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the “sanguinis group.” As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the “mitis group.” On the basis of the findings, we propose a novel group, named “sinensis group,” to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy.
Persistent Identifierhttp://hdl.handle.net/10722/211868
ISSN
2020 Impact Factor: 3.416
2015 SCImago Journal Rankings: 3.220
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorTeng, JLL-
dc.contributor.authorHuang, Y-
dc.contributor.authorTse, H-
dc.contributor.authorChen, JHK-
dc.contributor.authorTang, Y-
dc.contributor.authorLau, SKP-
dc.contributor.authorWoo, PCY-
dc.date.accessioned2015-07-21T02:14:09Z-
dc.date.available2015-07-21T02:14:09Z-
dc.date.issued2014-
dc.identifier.citationGenome Biology and Evolution, 2014, v. 6 n. 10, p. 2930-2943-
dc.identifier.issn1759-6653-
dc.identifier.urihttp://hdl.handle.net/10722/211868-
dc.description.abstractStreptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the “sanguinis group.” As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the “mitis group.” On the basis of the findings, we propose a novel group, named “sinensis group,” to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy.-
dc.languageeng-
dc.publisherOxford University Press for Society for Molecular Biology and Evolution. The Journal's web site is located at http://gbe.oxfordjournals.org-
dc.relation.ispartofGenome Biology and Evolution-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectStreptococcus sinensis-
dc.subjectGenome-
dc.subjectPhylogenomic-
dc.subject“Sinensis group”-
dc.subjectIllumina-
dc.titlePhylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus-
dc.typeArticle-
dc.identifier.emailTeng, JLL: llteng@hku.hk-
dc.identifier.emailTse, H: htse@hkucc.hku.hk-
dc.identifier.emailChen, JHK: jonchk@hku.hk-
dc.identifier.emailLau, SKP: skplau@hkucc.hku.hk-
dc.identifier.emailWoo, PCY: pcywoo@hkucc.hku.hk-
dc.identifier.authorityTeng, JLL=rp00277-
dc.identifier.authorityTse, H=rp00519-
dc.identifier.authorityLau, SKP=rp00486-
dc.identifier.authorityWoo, PCY=rp00430-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/gbe/evu232-
dc.identifier.pmid25331233-
dc.identifier.pmcidPMC4224358-
dc.identifier.scopuseid_2-s2.0-84931386247-
dc.identifier.hkuros245765-
dc.identifier.volume6-
dc.identifier.issue10-
dc.identifier.spage2930-
dc.identifier.epage2943-
dc.identifier.isiWOS:000346775800027-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl1759-6653-

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