Interstitial telomere-like repeats in the Arabidopsis thaliana genome.

Abstract

Eukaryotic chromosomal ends are protected by telomeres, which are thought to play an important role in ensuring the complete replication of chromosomes. On the other hand, non-functional telomere-like repeats in the interchromosomal regions (interstitial telomeric repeats; ITRs) have been reported in several eukaryotes. In this study, we identified eight ITRs in the Arabidopsis thaliana genome, each consisting of complete and degenerate 300-to 1200-bp sequences. The ITRs were grouped into three classes (class IA-B, class II, and class IIIA-E) based on the degeneracy of the telomeric repeats in ITRs. The telomeric repeats of the two ITRs in class I were conserved for the most part, whereas the single ITR in class II, and the five ITRs in class III were relatively degenerated. In addition, degenerate ITRs were surrounded by common sequences that shared 70-100% homology to each other; these are named ITR-adjacent sequences (IAS). Although the genomic regions around ITRs in class I lacked IAS, those around ITRs in class II contained IAS (IASa), and those around five ITRs in class III had nine types of IAS (IASb, c, d, e, f, g, h, i, and j). Ten IAS types in classes II and III showed no significant homology to each other. The chromosomal locations of ITRs and IAS were not category-related, but most of them were adjacent to, or part of, a centromere. These results show that the A. thaliana genome has undergone chromosomal rearrangements, such as end-fusions and segmental duplications.

The restriction endonuclease Tru9I is a useful tool to analyze telomere sequences separately from interstitial telomeric sequences in <i>Arabidopsis thaliana</i>

“…With regard to these results, Majerová and colleagues referred that: "This is, however, in a clear contradiction to the above mentioned data of Uchida et al [6] which provide an exact content of interstitial genomic regions comprising at least 3 telomeric repeats (to exclude random hits) as 20% of the total number telomeric repeats. Thus, according to genomic data, the ratio between terminal and interstitial telomeric repeats is almost reciprocal to that deduced in [4].…”

“…Since Arabidopsis telomeres are composed of perfect telomeric repeat arrays, they remain uncut after digestion with Tru9I. In contrast, ITSs are frequently cut because they are composed of very short arrays of perfect telomeric repeats interspersed with degenerated repeats [4][5][6][7]. When Arabidopsis genomic DNA is digested with Tru9I, resolved on an agarose gel and hybridized with a telomeric probe, most of the signals corresponding to ITSs disappear.…”

“…This discrepancy calls the results published in [4] correspond to telomeres but not to ITSs. They based this suggestion in a previous in silico study by Uchida and colleagues [6], where the authors made a classification/ quantification of the Arabidopsis ITSs containing three or more perfect telomeric repeats in tandem. Majerová and colleagues assumed that these are the only ITSs that should hybridize with a telomeric probe.…”

“…However, most of the ITSs present in the Arabidopsis genome contain degenerated repeats, being quite infrequent the presence of three or more tandem telomeric repeats at ITSs. For this reason, Uchida et al did not include in their study most of the ITSs present in the Arabidopsis genome, like those present in chromosome 4 [4,6]. Nevertheless, these degenerated ITSs can also hybridize with different degrees of efficiency with a telomeric probe.…”

Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in Panax ginseng

“…However, several studies have reported interstitial localization of telomeric repeats, like that observed in the interstitial region of chromosome 10. Interstitial telomeric sites have been demonstrated to be recombination hot-spots, genome rearrangement breakpoints, and even shown to be functional in several species (Day et al 1998;Hastie and Allshire 1989;Park et al 1992;Tremousaygue et al 1999;Uchida et al 2002). P. ginseng have undergone two major rounds of genome duplications (Choi et al 2013).…”