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Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

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Abstract

It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

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Acknowledgments

This work was supported by the European Commission within the Network of Excellence EVOLTREE (FP6-016322), INRA and Région Lorraine Council grants (project FORBOIS to FM). Dr. Labbé was supported by a Ph.D. scholarship from the Région Lorraine of France. We would like to thank Dr. Benoît Barrès, Dr. Pascal Frey, Axelle Andrieux and Christine Delaruelle (UMR IaM) for their assistance and helpful discussions, and Em Turner Chitty for the English proofreading. The INRA DNA sequencing facilities are funded by the Région Lorraine Council and the Institut Fédérateur 110.

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  1. Jessy Labbé

    Present address: Oak Ridge National Laboratory, 1 Bethel Valley Rd, MS-6034, Bldg. 1506, Oak Ridge, TN, 37831-6034, USA

Authors and Affiliations

  1. UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, INRA-Nancy, 54280, Champenoux, France

    Jessy Labbé, Claude Murat, Emmanuelle Morin, François Le Tacon & Francis Martin

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  1. Jessy Labbé
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Correspondence to Jessy Labbé.

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Communicated by U. Kues.

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Labbé, J., Murat, C., Morin, E. et al. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers. Curr Genet 57, 75–88 (2011). https://doi.org/10.1007/s00294-010-0328-9

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