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Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes

Nature Genetics volume 30, pages 194–200 (2002)Cite this article

Abstract

Microsatellites are a ubiquitous class of simple repetitive DNA sequence. An excess of such repetitive tracts has been described in all eukaryotes analyzed and is thought to result from the mutational effects of replication slippage1. Large-scale genomic and EST sequencing provides the opportunity to evaluate the abundance and relative distribution of microsatellites2 between transcribed and nontranscribed regions and the relationship of these features to haploid genome size. Although this has been studied in microbial and animal genomes3,4,5,6, information in plants is limited. We assessed microsatellite frequency in plant species with a 50-fold range in genome size that is mostly attributable to the recent amplification of repetitive DNA7. Among species, the overall frequency of microsatellites was inversely related to genome size and to the proportion of repetitive DNA but remained constant in the transcribed portion of the genome. This indicates that most microsatellites reside in regions pre-dating the recent genome expansion in many plants. The microsatellite frequency was higher in transcribed regions, especially in the untranslated portions, than in genomic DNA. Contrary to previous reports suggesting a preferential mechanism for the origin of microsatellites from repetitive DNA in both animals8,9 and plants10, our findings show a significant association with the low-copy fraction of plant genomes.

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Figure 1: Dinucleotide microsatellite frequencies in plants.
Figure 2: Frequency of microsatellites in relation to genome size and percentage of single-copy DNA.

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Acknowledgements

We thank B. Li, K. Henderson for the soybean and wheat libraries, M. Dolan and the DuPont Genomics group for technical help and J.A. Rafalski and B. Mazur for discussions and comments on the manuscript.

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  1. Wayne Powell

    Present address: Scottish Crop Research Institute, Invergowrie, Dundee, Scotland, UK

Authors and Affiliations

  1. E.I. duPont de Nemours and Co., DuPont Agriculture & Nutrition–Molecular Genetics, Newark, Delaware, USA

    Michele Morgante, Michael Hanafey & Wayne Powell

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  1. Michele Morgante
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Correspondence to Michele Morgante.

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Morgante, M., Hanafey, M. & Powell, W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30, 194–200 (2002). https://doi.org/10.1038/ng822

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