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The landscape of microbial phenotypic traits and associated genes

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dc.contributor.author Brbić, Maria
dc.contributor.author Piškorec, Martija
dc.contributor.author Vidulin, Vedrana
dc.contributor.author Krisko, Anita
dc.contributor.author Šmuc, Tomislav
dc.contributor.author Supek, Fran
dc.date.accessioned 2017-05-02T08:26:12Z
dc.date.available 2017-05-02T08:26:12Z
dc.date.issued 2016
dc.identifier.citation Brbić M, Piškorec M, Vidulin V, Kriško A, Šmuc T, Supek F. The landscape of microbial phenotypic traits and associated genes. Nucleic Acids Research. 2016;44(21):10074-90. DOI: 10.1093/nar/gkw964
dc.identifier.issn 1362-4962
dc.identifier.uri http://hdl.handle.net/10230/32075
dc.description.abstract Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text. Moreover, the ProTraits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in metagenomes. Notably, we find that gene synteny is highly predictive of many phenotypes, and highlight examples of gene neighborhoods associated with spore-forming ability. A global analysis of trait interrelatedness outlined clusters in the microbial phenotype network, suggesting common genetic underpinnings. Our extended set of phenotype annotations allows detection of 57 088 high confidence gene-trait links, which recover many known associations involving sporulation, flagella, catalase activity, aerobicity, photosynthesis and other traits. Over 99% of the commonly occurring gene families are involved in genetic interactions conditional on at least one phenotype, suggesting that epistasis has a major role in shaping microbial gene content.
dc.description.sponsorship This work was funded by the Croatian Science Foundation grants HRZZ-9623 (DescriptiveInduction) and HRZZ-5660 (MultiCaST) and by the European Union FP7 grants ICT-2013-612944 (MAESTRA) and REGPOT-2012-2013-1-316289 (InnoMol). FS acknowledges the support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ (SEV-2012-0208) and the FP7 project 4DCellFate (277899). Funding for open access charge: EU FP7 FET ICT-2013-612944 (MAESTRA).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Nucleic Acids Research. 2016;44(21):10074-90
dc.rights © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.subject.other Genòmica
dc.subject.other Fenotip
dc.title The landscape of microbial phenotypic traits and associated genes
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkw964
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/612944
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/277899
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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