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Open Access Highly Accessed Research article

Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

Jean-Francois Martin1*, Nicolas Pech2, Emese Meglécz2, Stéphanie Ferreira3, Caroline Costedoat2, Vincent Dubut2, Thibaut Malausa4 and André Gilles2

Author Affiliations

1 Centre de biologie et de gestion des Populations (Montpellier SupAgro, INRA, IRD, CIRAD), Campus International de Baillarguet, CS30016, Montferrier sur Lez cedex, France

2 Aix-Marseille Université, CNRS, IRD, UMR 6116 - IMEP, Equipe Evolution Génome Environnement, Centre Saint-Charles, Case 36, 3 place Victor Hugo, 13331 Marseille Cedex 3, France

3 Genoscreen, Genomic Platform and R&D, Campus de l'Institut Pasteur, 1 rue du Professeur Calmette, Bâtiment Guérin, 4ème étage, 59000 Lille, France

4 Institut National de la Recherche Agronomique, UMR 1301, Equipe BPI, 400 route des Chappes, BP 167, 06903 Sophia-Antipolis Cedex, France

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BMC Genomics 2010, 11:560  doi:10.1186/1471-2164-11-560

Published: 12 October 2010

Abstract

Background

Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (Apis mellifera and Danio rerio), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes.

Results

The A. mellifera genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase.

Conclusions

This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.