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hal.structure.identifierUniversité de Liège
dc.contributor.authorVERDU, Cindy F.
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGUICHOUX, Erwan
hal.structure.identifierUniversité de Liège
dc.contributor.authorQUEVAUVILLERS, Samuel
hal.structure.identifierUniversité de Liège
dc.contributor.authorDE THIER, Olivier
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLAIZET, Yec'Han
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDELCAMP, Adline
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorGEVAUDANT, Frederic
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierBiodiversity and Landscape Unit, Gembloux Agro-Bio Tech
dc.contributor.authorMONTY, Arnaud
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPORTE, Annabel J.
hal.structure.identifierBiodiversity and Landscape Unit, Gembloux Agro-Bio Tech
dc.contributor.authorLEJEUNE, Philippe
hal.structure.identifierUniversité de Liège
dc.contributor.authorLASSOIS, Ludivine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorMARIETTE, Stéphanie
dc.date.issued2016
dc.description.abstractEnThe RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.
dc.language.isoen
dc.publisherWiley Open Access
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enblack locust
dc.subject.endepth of coverage
dc.subject.enputative paralogy filtering
dc.subject.enrestriction site-associated DNA sequencing
dc.title.enDealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
dc.typeArticle de revue
dc.identifier.doi10.1002/ece3.2466
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences de l'environnement
bordeaux.journalEcology and Evolution
bordeaux.page7323-7333
bordeaux.volume6
bordeaux.issue20
bordeaux.peerReviewedoui
hal.identifierhal-02634478
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02634478v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Ecology%20and%20Evolution&rft.date=2016&rft.volume=6&rft.issue=20&rft.spage=7323-7333&rft.epage=7323-7333&rft.au=VERDU,%20Cindy%20F.&GUICHOUX,%20Erwan&QUEVAUVILLERS,%20Samuel&DE%20THIER,%20Olivier&LAIZET,%20Yec'Han&rft.genre=article


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