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doi:10.1534/genetics.105.055202
A more recent version of this article appeared on May 1, 2006.
REGULAR RESEARCH PAPERS |
Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end
Hui-Fen Kuo 1, Kenneth M Olsen 1 and Eric J Richards 1*
1 Washington University
* To whom correspondence should be addressed. E-mail: richards{at}biology.wustl.edu.
Submitted on December 26, 2005
Revised on February 2, 2006
Accepted on 7 March 2006
We investigated genome dynamics at a chromosome end in the model plant A. thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric region of chromosome 1 north (~3.5 kb), which exemplifies the simple organization of subtelomeric regions in this species. PCR fragment-length variation across the subtelomeric region indicated that the 1.4 kb distal region showed elevated structural variation relative to the centromere-proximal region. Examination of nucleotide sequences from this 1.4 kb region revealed diverse DNA rearrangements, including an inversion, several deletions, and an insertion of a retrotransposon LTR. The structures at the deletion and inversion breakpoints are characteristic of simple deletion-associated non-homologous-end-joining (NHEJ). There was strong linkage disequilibrium between the distal subtelomeric region and the proximal telomere, which contains degenerate and variant telomeric repeats. Variation in the proximal telomere was characterized by the expansion and deletion of blocks of repeats. Our sample of accessions documented two independent chromosome healing events associated with terminal deletions of the subtelomeric region, as well as the capture of a reshuffled mitochondrial DNA segment in the proximal telomeric array. This natural variation study highlights the variety of genomic events that drive the fluidity of chromosome termini.
Key Words: Chromosome healing, Organellor DNA transfer to the nuclear genome, Subtelomeric region, Telomere
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