High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries

Thibaut Malausa (1) , André Gilles (2) , Emese Meglécz (2) , Hélène Blancard (3) , Stéphanie Duthoy (3) , Caroline Costedoat (2) , Vincent Dubut (2) , Nicolas Pech (2) , Philippe Castagnone-Sereno (1) , Christophe Delye (1) , Nicolas Feau (4) , Pascal Frey (5) , Philippe Gauthier (6) , Thomas Guillemaud (7) , Laurent Hazard (8) , Valérie Le Corre (9) , Brigitte Lung (4) , Pierre-Jean Male (6) , Stéphanie Ferreira (3) , Jean-François Martin (6)

1 IBSV - Interactions Biotiques et Santé Végétale
2 AMU - Aix Marseille Université
3 Genoscreen
4 BioGeCo - Biodiversité, Gènes & Communautés
5 IAM - Interactions Arbres-Microorganismes
6 UMR CBGP - Centre de Biologie pour la Gestion des Populations
7 ISA - Institut Sophia Agrobiotech
8 AGIR - AGroécologie, Innovations, teRritoires
9 FLAVIC - FLAveur, VIsion et Comportement du consommateur

Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11 497 to 34 483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms.

Mots clés: microsatellite repeats; primer design; pyrosequencing; enriched library; genetic marker; genotyping; microsatellite isolation; next-generation sequencing; taxonomy

Mots clés: marqueur microsatellite; génotypage; pyroséquençage; banque d'adn; taxonomie; pcr; marqueur génétique

Domaines: Sciences du Vivant [q-bio]

Thibaut Malausa, André Gilles, Emese Meglécz, Hélène Blancard, Stéphanie Duthoy, et al.. High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Molecular Ecology Resources, 2011, 11 (4), pp.638-644. ⟨10.1111/j.1755-0998.2011.02992.x⟩. ⟨hal-01506135⟩