Abstract
BackgroundSatellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes.ResultsWe performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths.ConclusionThis work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.
Highlights
Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome
We addressed some of the questions raised above by investigating the occurrence and properties of extrachromosomal circular DNA (eccDNA) molecules derived from satellite repeats in a range of species from three genera of higher plants (Fabaceae, Poaceae, Brassicaceae)
We did not observe significant differences in eccDNA signals between these samples, suggesting that there are comparable levels of circular molecules derived from FokI satellite in all investigated V. faba tissues and that these levels are not significantly affected by stress conditions
Summary
Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. BMC Plant Biology 2008, 8:90 http://www.biomedcentral.com/1471-2229/8/90 repeats undergo rapid evolutionary changes of their sequences and abundance, leading to the frequent occurrence of genus- or species-specific families of satellite DNA [2,3,4,5] Contrary to this diversification observed between various taxa, the repeat monomers are usually well-homogenized within a species. It has been proposed that they involve extrachromosomal circular DNA (eccDNA) molecules, arising from intrastrand recombination between monomers within satellite arrays and subsequently serving as a template for rollingcircle replication This process would result in the synthesis of linear DNA fragments composed of multiple copies of the circular template molecules and their reintegration into the genome, providing an efficient mechanism for amplification and eventual sequence homogenization of satDNA
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