Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome

Abstract

      <p>
        Background
        <p>Retrotransposons are mobile DNA elements that spread through genomes via the action of element-encoded reverse transcriptases. They are ubiquitous constituents of most eukaryotic genomes, especially those of higher plants. The pericentromeric regions of soybean (<i>Glycine max</i>) chromosomes contain &gt;3,200 intact copies of the Gmr9/GmOgre retrotransposon. Between the 3' end of the coding region and the long terminal repeat, this retrotransposon family contains a polymorphic minisatellite region composed of five distinct, interleaved minisatellite families. To better understand the possible role and origin of retrotransposon-associated minisatellites, a computational project to map and physically characterize all members of these families in the <i>G. max</i> genome, irrespective of their association with Gmr9, was undertaken.</p>
      </p>
      <p>
        Methods
        <p>A computational pipeline was developed to map and analyze the organization and distribution of five Gmr9-associated minisatellites throughout the soybean genome. Polymerase chain reaction amplifications were used to experimentally assess the computational outputs.</p>
      </p>
      <p>
        Results
        <p>A total of 63,841 copies of Gmr9-associated minisatellites were recovered from the assembled <i>G. max</i> genome. Ninety percent were associated with Gmr9, an additional 9% with other annotated retrotransposons, and 1% with uncharacterized repetitive DNAs. Monomers were tandemly interleaved and repeated up to 149 times per locus.</p>
      </p>
      <p>
        Conclusions
        <p>The computational pipeline enabled a fast, accurate, and detailed characterization of known minisatellites in a large, downloaded DNA database, and PCR amplification supported the general organization of these arrays.</p>
      </p>

Reply by Email