Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants
Corresponding Author
Sarit Cohen
Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel, and
(fax +972 36409407; e-mail [email protected]).Search for more papers by this authorAndreas Houben
Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
Search for more papers by this authorDaniel Segal
Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel, and
Search for more papers by this authorCorresponding Author
Sarit Cohen
Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel, and
(fax +972 36409407; e-mail [email protected]).Search for more papers by this authorAndreas Houben
Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
Search for more papers by this authorDaniel Segal
Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel, and
Search for more papers by this authorSummary
Extrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It was found in various non-plant organisms from yeast to humans. EccDNA is heterogeneous in size and contains sequences derived primarily from repetitive chromosomal DNA. Here, we report the occurrence of eccDNA in small and large genome plant species, as identified using two-dimensional gel electrophoresis. We show that eccDNA is readily detected in both Arabidopsis thaliana and Brachycome dichromosomatica, reflecting a normal phenomenon that occurs in wild-type plants. The size of plant eccDNA ranges from > 2 kb to < 20 kb, which is similar to the sizes found in other organisms. These DNA molecules correspond to 5S ribosomal DNA (rDNA), non-coding chromosomal high-copy tandem repeats and telomeric DNA of both species. Circular multimers of the repeating unit of 5S rDNA were identified in both species. In addition, similar multimers were also demonstrated with the B. dichromosomatica repetitive element Bdm29. Such circular multimers of tandem repeats were found in animal models, suggesting a common mechanism for eccDNA formation among eukaryotes. This mechanism may involve looping-out via intrachromosomal homologous recombination. The implications of these results on genome plasticity and evolutionary processes are discussed.
Supporting Information
Figure S1. Tandem organization of 5S ribosomal DNA (rDNA) genes in Brachycome dichromosomatica. Genomic DNA preparations from five different wild-type plants of Brachycome were partially digested with BamHI. The gel was blotted and hybridized with Brachycome 5S rDNA probe. Ladders of bands indicate the tandem organization of a ca 500-bp repeating unit in all plants.
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