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Fast sequence-based microsatellite genotyping development workflow

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierEcologie Comportementale et Biologie des Populations de Poissons [ECOBIOP]
dc.contributor.authorLEPAIS, Olivier
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorCHANCEREL, Emilie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBOURY, Christophe
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorSALIN, Franck
hal.structure.identifierEcologie Comportementale et Biologie des Populations de Poissons [ECOBIOP]
dc.contributor.authorMANICKI, Aurélie
hal.structure.identifierEcologie Comportementale et Biologie des Populations de Poissons [ECOBIOP]
dc.contributor.authorTAILLEBOIS, Laura
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDUTECH, Cyril
hal.structure.identifierUniversity of Batna Hadj Lakhder [Algeria]
dc.contributor.authorAISSI, Abdeldjalil
hal.structure.identifierEcologie Comportementale et Biologie des Populations de Poissons [ECOBIOP]
dc.contributor.authorBACLES, Cécile
hal.structure.identifierEcosystèmes aquatiques et changements globaux [UR EABX]
dc.contributor.authorDAVERAT, Françoise
hal.structure.identifierÉcologie et santé des écosystèmes [ESE]
dc.contributor.authorLAUNEY, Sophie
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGUICHOUX, Erwan
dc.date.issued2020
dc.identifier.issn2167-8359
dc.description.abstractEnApplication of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
dc.description.sponsorshipPlateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur "
dc.language.isoen
dc.publisherPeerJ
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enSubjects Conservation Biology
dc.subject.enEcology
dc.subject.enEvolutionary Studies
dc.subject.enGenetics
dc.subject.enPopulation Biology Keywords Sequence-based microsatellite genotyping
dc.subject.enSSR-GBS
dc.subject.enSSR-seq
dc.subject.enHaplotype sequence
dc.subject.enHapSTR
dc.subject.enSNPSTR
dc.title.enFast sequence-based microsatellite genotyping development workflow
dc.typeArticle de revue
dc.identifier.doi10.7717/peerj.9085
dc.subject.halSciences de l'environnement
bordeaux.journalPeerJ
bordeaux.page1-28
bordeaux.volume8
bordeaux.peerReviewedoui
hal.identifierhal-02936408
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02936408v1
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