title: Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome.
abstract: BACKGROUND
  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 (Glycine max) chromosomes contain >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 G. max genome, irrespective of their association with Gmr9, was undertaken.
  
  
  METHODS
  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.
  
  
  RESULTS
  A total of 63,841 copies of Gmr9-associated minisatellites were recovered from the assembled G. max 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Program in Bioinformatics, Loyola University Chicago, 1032 W, Sheridan Rd, Chicago, IL 60660, USA.
authors.forename: Lauren S
authors.initials: LS
authors.lastname: Mogil
authors.forename: Kamil
authors.initials: K
authors.lastname: Slowikowski
authors.forename: Howard M
authors.initials: HM
authors.lastname: Laten
mesh_terms: D002874:Chromosome Mapping; D018744:DNA, Plant / Q000737:chemistry; D018745:Genome, Plant; D018598:Minisatellite Repeats; D018626:Retroelements; D013025:Glycine max / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D018626:Retroelements