Evolution of Tandemly Repeated Sequences: What Happens at the End of an Array?

Abstract

Abstract. Tandemly repeated sequences are a major component of the eukaryotic genome. Although the general characteristics of tandem repeats have been well documented, the processes involved in their origin and maintenance remain unknown. In this study, a region on the paternal sex ratio (PSR) chromosome was analyzed to investigate the mechanisms of tandem repeat evolution. The region contains a junction between a tandem array of PSR2 repeats and a copy of the retrotransposon NATE, with other dispersed repeats (putative mobile elements) on the other side of the element. Little similarity was detected between the sequence of PSR2 and the region of NATE flanking the array, indicating that the PSR2 repeat did not originate from the underlying NATE sequence. However, a short region of sequence similarity (11/15 bp) and an inverted region of sequence identity (8 bp) are present on either side of the junction. These short sequences may have facilitated nonhomologous recombination between NATE and PSR2, resulting in the formation of the junction. Adjacent to the junction, the three most terminal repeats in the PSR2 array exhibited a higher sequence divergence relative to internal repeats, which is consistent with a theoretical prediction of the unequal exchange model for tandem repeat evolution. Other NATE insertion sites were characterized which show proximity to both tandem repeats and complex DNAs containing additional dispersed repeats. An ''accretion model'' is proposed to account for this association by the accumulation of mobile elements at the ends of tandem arrays and into ''islands'' within arrays. Mobile elements inserting into arrays will tend to migrate into islands and to array ends, due to the turnover in the number of intervening repeats.

Modular evolution of egg case silk genes across orb-weaving spider superfamilies

“…As observed in other silk sequences (28), the final repeat in each TuSp1 sequence (repeat 1s, Fig. 1 A) was least similar to upstream repeats, consistent with predictions of the unequal exchange model for tandem repeat evolution (34,35).…”

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species

“…The model also predicts that repeats immediately adjacent to satDNA Â satDNA or satDNA Â non-satDNA junctions should present higher levels of sequence divergence compared to repeats from more central regions of the array, where unequal crossing-over is more likely to happen. There are very limited data sets on the literature concerning the analysis of satDNA junctions under this context, but they generally support the expectations of the model (McAllister and Werren, 1999;Schueler et al, 2001;Mravinac and Plohl, 2007). The homogeneity of a junction between the AATAT and TTCTC satellites in the D. melanogaster Dp1187 minichromosome is an exception (Sun et al, 2003).…”

“…Whole-genome projects have many sharp junctions of satellites with generally uncharacterized genomic DNA, although accurate assembly of individual sequence reads into satDNA arrays may be extremely difficult (see Lee et al, 2006 for care required for assembly of blocks of HORs). Nevertheless, in examples that have been verified, abrupt transitions involving satDNA Â satDNA or satDNA Â defined non-satDNA junctions have been reported in a number of organisms, such as humans (Gaff et al, 1994), plants (Alkhimova et al, 2004;Lee et al, 2006) and insects (McAllister and Werren, 1999;Sun et al, 2003;Krzywinski et al, 2005).…”

An ITS Phylogeny of Leccinum and an Analysis of the Evolution of Minisatellite-like Sequences within ITS1

“…However, since the flanking regions seem to be relatively conserved, there are not much variable sites found in these regions anyway. Moreover, unequal crossing over does not necessarily imply recombination in the flanking regions (McAllister and Werren 1999). Neither the patterns found by mapping the core sequences, nor the Tandem Repeats Finder analyses, revealed patterns that lead to the conclusion that SSM is not the most probable process responsible for the length polymorphisms found.…”