Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification

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dc.citation.journalTitleEcology And Evolution
dc.contributor.authorFranco-Sierra, N.D.
dc.contributor.authorDíaz-Nieto, J.F.
dc.contributor.departmentUniversidad EAFIT. Departamento de Cienciasspa
dc.contributor.researchgroupBiodiversidad, Evolución y Conservaciónspa
dc.date.accessioned2021-03-23T19:52:10Z
dc.date.available2021-03-23T19:52:10Z
dc.date.issued2020-01-01
dc.description.abstractMolecular information is crucial for species identification when facing challenging morphology-based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers are not available, problems in reaction standardization), amplification-free approaches could be an optimal alternative. Recent advances in DNA sequencing, like the MinION device from Oxford Nanopore Technologies (ONT), allow to obtain genomic data with low laboratory and technical requirements, and at a relatively low cost. In this study, we explore ONT sequencing for molecular species identification from a total DNA sample obtained from a neotropical rodent and we also test the technology for complete mitochondrial genome reconstruction via genome skimming. We were able to obtain “de novo” the complete mitogenome of a specimen from the genus Melanomys (Cricetidae: Sigmodontinae) with average depth coverage of 78X using ONT-only data and by combining multiple assembly routines. Our pipeline for an automated species identification was able to identify the sample using unassembled sequence data (raw) in a reasonable computing time, which was substantially reduced when a priori information related to the organism identity was known. Our findings suggest ONT sequencing as a suitable candidate to solve species identification problems in metazoan nonmodel organisms and generate complete mtDNA datasets. © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.eng
dc.formatapplication/pdf
dc.identifierhttps://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=11940
dc.identifier.doi10.1002/ece3.6151
dc.identifier.issn20457758
dc.identifier.otherWOS;000524417200032
dc.identifier.otherPUBMED;32274008
dc.identifier.otherSCOPUS;2-s2.0-85081324341
dc.identifier.urihttp://hdl.handle.net/10784/26757
dc.language.isoengeng
dc.publisherJohn Wiley and Sons Ltd
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85081324341&doi=10.1002%2fece3.6151&partnerID=40&md5=74fbbc2005752ac07686ef84648602b2
dc.rightshttps://v2.sherpa.ac.uk/id/publication/20794
dc.rights.accessrightsinfo:eu-repo/semantics/openAccesseng
dc.rights.localAcceso abiertospa
dc.sourceEcology And Evolution
dc.subjectgenomeeng
dc.subjectskimmingeng
dc.subjectMinIONeng
dc.subjectmitochondrialeng
dc.subjectDNAeng
dc.subjectsequencingeng
dc.subjectmoleculareng
dc.subjectspecieseng
dc.subjectidentificationeng
dc.subjectvertebrateeng
dc.subjectspecieseng
dc.subjectidentificationeng
dc.titleRapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identificationeng
dc.typepublishedVersioneng
dc.typeinfo:eu-repo/semantics/publishedVersioneng
dc.typearticleeng
dc.typeinfo:eu-repo/semantics/articleeng
dc.type.localArtículospa

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