A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

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dc.contributor.authorVartia, Salla
dc.contributor.authorVillanueva-Cañas, José L.
dc.contributor.authorFinarelli, John
dc.contributor.authorFarrell, Edward D.
dc.contributor.authorCollins, Patrick C.
dc.contributor.authorHughes, Graham M.
dc.contributor.authorCarlsson, Jeanette E. L.
dc.contributor.authorGauthier, David T.
dc.contributor.authorMcGinnity, Philip
dc.contributor.authorCross, Thomas F.
dc.contributor.authorFitzgerald, Richard D.
dc.contributor.authorMirimin, Luca
dc.contributor.authorCrispie, Fiona
dc.contributor.authorCotter, Paul D.
dc.contributor.authorCarlsson, Jens
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderIrish Research Councilen
dc.contributor.funderMarine Instituteen
dc.contributor.funderEuropean Regional Development Funden
dc.contributor.funderMinisterio de Economía y Competitividaden
dc.date.accessioned2018-03-27T12:04:40Z
dc.date.available2018-03-27T12:04:40Z
dc.date.issued2016-01-20
dc.date.updated2018-03-14T09:14:00Z
dc.description.abstractThis study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.en
dc.description.sponsorshipScience Foundation Ireland (SFI 12/IP/1308); Irish Research Council (Ref No. GOIPD/2013/320; Graduate Research Education Programme); Marine Institute and European Regional Development Fund (Grant-Aid Agreement No. PBA/AF/07/004, EIRCOD); Ministerio de Economía y Competitividad (FPI BES-2010–038494; EEBB-I-13–06270)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid150565
dc.identifier.citationVartia, S., Villanueva-Cañas, J. L., Finarelli, J., Farrell, E. D., Collins, P. C., Hughes, G. M., Carlsson, J. E. L., Gauthier, D. T., McGinnity, P., Cross, T. F., FitzGerald, R. D., Mirimin, L., Crispie, F., Cotter, P. D. and Carlsson, J. (2016) 'A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding', Royal Society Open Science, 3, 150565 (9pp). doi:10.1098/rsos.150565en
dc.identifier.doi10.1098/rsos.150565
dc.identifier.endpage9en
dc.identifier.issn2054-5703
dc.identifier.journaltitleRoyal Society Open Scienceen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/5701
dc.identifier.volume3en
dc.language.isoenen
dc.publisherRoyal Societyen
dc.relation.urihttps://github.com/egenomics/micomba
dc.rights© 2016, the Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectAmplicon sequencingen
dc.subjectGadus morhuen
dc.subjectGenotyping by sequencingen
dc.subjectNext-generation sequencingen
dc.subjectUniversal primeren
dc.subjectSingle-nucleotide polymorphismsen
dc.subjectPopulation parametersen
dc.subjectModel selectionen
dc.subjectComplete genomeen
dc.subjectHomoplasyen
dc.subjectLocien
dc.subjectEvolutionen
dc.subjectPlatformen
dc.titleA novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcodingen
dc.typeArticle (peer-reviewed)en
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