Institute of Genome Research, University of Bielefeld, D-33594 Bielefeld, Germany.
BMC Plant Biol. 2010 Jan 11;10:8. doi: 10.1186/1471-2229-10-8.
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.
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.
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.
重复 DNA 是真核生物基因组的主要组成部分，尤其在植物中经常出现。目前，甜菜（Beta vulgaris）基因组的测序正在进行中，对重复 DNA 序列的了解对于基因组注释至关重要。我们生成了一个 c0t-1 文库，代表高度到中度重复序列，用于鉴定主要的 B. vulgaris 重复家族。虽然高度丰富的卫星序列已有很好的描述，但在植物中，微卫星序列的研究还很不完善。因此，我们专注于鉴定和表征这些串联重复序列。
对 1763 个 c0t-1 DNA 片段的分析，提供了 442 kb 的序列数据，表明 pBV 和 pEV 卫星是 B. vulgaris 基因组中最丰富的重复家族，而其他先前描述的重复序列的拷贝数较低。我们分离了 517 个新的重复序列，并使用这部分序列鉴定微卫星和新的卫星家族。生物信息学分析和 Southern 杂交表明，微卫星在 B. vulgaris 中中度到高度扩增。FISH 显示它们在大多数染色体上呈弥散定位，聚集成大小和数量不等的数组，在特定区域存在缺失和耗尽。
c0t-1 文库代表了 B. vulgaris 基因组的主要重复家族，对 c0t-1 DNA 的分析被证明是鉴定微卫星的有效方法。我们建立了迄今为止植物中微卫星最广泛的分析，并观察到它们在染色体上的定位，为甜菜基因组的注释以及植物基因组中微卫星进化的理解提供了背景。
