LEPAIS, Olivier; CHANCEREL, Emilie; BOURY, Christophe; SALIN, Franck; MANICKI, Aurélie; TAILLEBOIS, Laura; DUTECH, Cyril; AISSI, Abdeldjalil; BACLES, Cécile; DAVERAT, Françoise; LAUNEY, Sophie; GUICHOUX, Erwan

doi:10.7717/peerj.9085

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LEPAIS, Olivier
Biodiversité, Gènes & Communautés [BioGeCo]
Ecologie Comportementale et Biologie des Populations de Poissons [ECOBIOP]

CHANCEREL, Emilie
Biodiversité, Gènes & Communautés [BioGeCo]

BOURY, Christophe
Biodiversité, Gènes & Communautés [BioGeCo]

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Article de revue

Ce document a été publié dans

PeerJ. 2020, vol. 8, p. 1-28

PeerJ

Résumé en anglais

Application 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.< Réduire

Mots clés en anglais

Subjects Conservation Biology

Ecology

Evolutionary Studies

Genetics

Population Biology Keywords Sequence-based microsatellite genotyping

SSR-GBS

SSR-seq

Haplotype sequence

HapSTR

SNPSTR

DOI

http://dx.doi.org/10.7717/peerj.9085

Project ANR

Plateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur " - ANR-10-EQPX-0016

Origine

Importé de hal

Unités de recherche

BioGeCo (Biodiversité Gènes & Communautés) - UMR 1202