A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature

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dc.contributor.authorMarakeby, Haithamen
dc.contributor.authorBadr, Emanen
dc.contributor.authorTorkey, Hanaaen
dc.contributor.authorSong, Yuhyunen
dc.contributor.authorLeman, Scotland C.en
dc.contributor.authorMonteil, Caroline L.en
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.authorVinatzer, Boris A.en
dc.contributor.departmentCivil and Environmental Engineeringen
dc.contributor.departmentStatisticsen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2016-09-15T02:10:56Zen
dc.date.available2016-09-15T02:10:56Zen
dc.date.issued2014-02-21en
dc.description.abstractA broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. The current system is thus inadequate to classify and name the immense genetic diversity within species that is now being revealed by genome sequencing on a daily basis. To address this lack of a general intra-species classification and naming system adequate for today’s speed of discovery of new diversity, we propose a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis. We provide examples demonstrating that genome similarity-based codes largely align with current taxonomic groups at many different levels in bacteria, animals, humans, plants, and viruses. Importantly, the proposed approach is only slightly affected by the order of code assignment and can thus provide codes that reflect similarity between organisms and that do not need to be revised upon discovery of new diversity. We envision genome similarity-based codes to complement current biological nomenclature and to provide a universal means to communicate unambiguously about any genome-sequenced organism in fields as diverse as biodiversity research, infectious disease control, human and microbial forensics, animal breed and plant cultivar certification, and human ancestry research.en
dc.description.versionPublished versionen
dc.format.extent? - ? (12) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0089142en
dc.identifier.issn1932-6203en
dc.identifier.issue2en
dc.identifier.urihttp://hdl.handle.net/10919/72945en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherPLOSen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000331717900057&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjecthuman mitochondrial-dnaen
dc.subjectspecies definitionen
dc.subjectprokaryotesen
dc.subjectphylogenyen
dc.titleA System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclatureen
dc.title.serialPLOS ONEen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Plant Pathology, Physiology, & Weed Scienceen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen

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