Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris.
BACKGROUND
Repetitive DNA is a major fraction of eukaryotic genomes and occurs particularly often in plants. Currently, the sequencing of the sugar beet (Beta vulgaris) genome is under way and knowledge of repetitive DNA sequences is critical for the genome annotation. We generated a c0t-1 library, representing highly to moderately repetitive sequences, for the characterization of the major B. vulgaris repeat families. While highly abundant satellites are well-described, minisatellites are only poorly investigated in plants. Therefore, we focused on the identification and characterization of these tandemly repeated sequences.


RESULTS
Analysis of 1763 c0t-1 DNA fragments, providing 442 kb sequence data, shows that the satellites pBV and pEV are the most abundant repeat families in the B. vulgaris genome while other previously described repeats show lower copy numbers. We isolated 517 novel repetitive sequences and used this fraction for the identification of minisatellite and novel satellite families. Bioinformatic analysis and Southern hybridization revealed that minisatellites are moderately to highly amplified in B. vulgaris. FISH showed a dispersed localization along most chromosomes clustering in arrays of variable size and number with exclusion and depletion in distinct regions.


CONCLUSIONS
The c0t-1 library represents major repeat families of the B. vulgaris genome, and analysis of the c0t-1 DNA was proven to be an efficient method for identification of minisatellites. We established, so far, the broadest analysis of minisatellites in plants and observed their chromosomal localization providing a background for the annotation of the sugar beet genome and for the understanding of the evolution of minisatellites in plant genomes.
Zakrzewski
Falk
F
Institute of Genome Research, University of Bielefeld, D-33594 Bielefeld, Germany.
Wenke
Torsten
T
Holtgräwe
Daniela
D
Weisshaar
Bernd
B
Schmidt
Thomas
T
D027461:Beta vulgaris / Q000235:genetics*; D032461:Chromosomes, Plant; D019295:Computational Biology / Q000379:methods; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D018598:Minisatellite Repeats; D020161:Physical Chromosome Mapping; D017422:Sequence Analysis, DNA
D018744:DNA, Plant