Natural Variation in a Subtelomeric Region of Arabidopsis: Implications for the Genomic Dynamics of a Chromosome End

Abstract

We investigated genome dynamics at a chromosome end in the model plant Arabidopsis 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 represents the relatively 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 nonhomologous endjoining (NHEJ) events. 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 scrambled 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.

Suppression of RICE TELOMERE BINDING PROTEIN1 Results in Severe and Gradual Developmental Defects Accompanied by Genome Instability in Rice

“…In addition, analysis of the subtelomeric region of 35 wild-type accessions revealed higher structural variation relative to centromere region, which implies the variety of genomic events that drive the fluidity of chromosome termini (Kuo et al, 2006). Maillet et al (2006) These recent studies support the notion that plant telomeres are structurally and functionally dynamic.…”

Cloning of the Papaya Chromoplast-Specific Lycopene β-Cyclase, CpCYC-b, Controlling Fruit Flesh Color Reveals Conserved Microsynteny and a Recombination Hot Spot

“…This insertion of two Ts after five Ts could be the result of replication slippage during meiosis ( Fig. 1; Karthikeyan et al, 1999;Ball et al, 2005;Kuo et al, 2006). The mRNA transcripts for CpCYC-b and CpCHY-b are detectable in low levels from developing red-fleshed papaya (Fig.…”

Molecular Analysis of a Large Subtelomeric Nucleotide-Binding-Site–Leucine-Rich-Repeat Family in Two Representative Genotypes of the Major Gene Pools of Phaseolus vulgaris

“…However, systematic localization of large R gene clusters in subtelomeric regions is not always observed, for example, in the A. thaliana genome (Meyers et al 2003). In addition, subtelomeric regions in A. thaliana do not share extensive similarity among most nonhomologous chromosomes, such as seen in yeast and humans (Kuo et al 2006). This suggests that additional data are needed to understand the behavior of subtelomeric regions in plants (Fan et al 2008) and that A. thaliana may not be representative of all plant species.…”