Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications

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• dc.contributor.author Stavrou, Aimilia A.
• dc.contributor.author Mixão, Verónica
• dc.contributor.author Boekhout, Teun
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.date.accessioned 2019-12-10T08:42:33Z
• dc.date.available 2019-12-10T08:42:33Z
• dc.date.issued 2018
• dc.description.abstract Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole-genome shotgun data. Analyses of phylogenetic markers, read mapping and single nucleotide polymorphisms served to correct the identification. We propose that the routine use of such analyses could help to detect misidentifications arising from unsupervised analyses and correct them before they enter the databases. Finally, we discuss broader implications of such misidentifications and the difficulty of correcting them once they are in the records.
• dc.description.sponsorship This work has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie grant agreement no. H2020‐MSCA‐ITN‐2014‐642095, ‘OPATHY’. T.G. acknowledges support from the Spanish Ministry of Economy and Competitiveness grant BFU2015‐67107 cofounded by European Regional Development Fund; from the European Union and ERC Seventh Framework Programme (FP7/2007‐2013) under grant agreement ERC‐2012‐StG‐310325; from the Catalan Research Agency (AGAUR) SGR857; and from the CERCA Programme/Generalitat de Catalunya. The authors declare that there is no conflict of interest.
• dc.format.mimetype application/pdf
• dc.identifier.citation Stavrou AA, Mixão V, Boekhout T, Gabaldón T. Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications. Yeast. 2018;35(6):425-9. DOI: 10.1002/yea.3303
• dc.identifier.doi http://dx.doi.org/10.1002/yea.3303
• dc.identifier.issn 0749-503X
• dc.identifier.uri http://hdl.handle.net/10230/43130
• dc.language.iso eng
• dc.publisher Wiley
• dc.relation.ispartof Yeast. 2018;35(6):425-9
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/642095
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015‐67107
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/310325
• dc.rights © 2018 The Authors. Yeast published by John Wiley & Sons, Ltd. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.keyword Candida albicans
• dc.subject.keyword Naumovozyma dairenensis
• dc.subject.keyword Misidentification
• dc.subject.keyword Public databases
• dc.title Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion