Expansion of microsatellites on evolutionary young Y chromosome.

Sex chromosomes are an ideal system to study processes connected with suppressed recombination. We found evidence of microsatellite expansion, on the relatively young Y chromosome of the dioecious plant sorrel (Rumex acetosa, XY1Y2 system), but no such expansion on the more ancient Y chromosomes of liverwort (Marchantia polymorpha) and human. The most expanding motifs were AC and AAC, which also showed periodicity of array length, indicating the importance of beginnings and ends of arrays. Our data indicate that abundance of microsatellites in genomes depends on the inherent expansion potential of specific motifs, which could be related to their stability and ability to adopt unusual DNA conformations. We also found that the abundance of microsatellites is higher in the neighborhood of transposable elements (TEs) suggesting that microsatellites are probably targets for TE insertions. This evidence suggests that microsatellite expansion is an early event shaping the Y chromosome where this process is not opposed by recombination, while accumulation of TEs and chromosome shrinkage predominate later

The length distribution of selected microsatellite arrays in human chromosomes.

<p>The analysis of all human chromosomes showing abundance of AC/CA (A), TG/GT (B), AAC/ACA/CAA (C) and GTT/TGT/TTG (D) microsatellite arrays plotted against their length.</p

The length distribution of microsatellite arrays AC and AAC.

<p>The length of AC and AAC microsatellite arrays in <i>Rumex acetosa</i> (A and B, respectively), <i>Marchantia polymorpha</i> (C and D) and human (E–H) plotted against arrays abundance determined from 454 sequencing data (A–F) or continual sequence (G, H) calculated per 100 Mb. Males are in blue, females are in red.</p

Fluorescent <i>in situ</i> hybridization of mitotic metaphase chromosomes of male <i>Rumex acetosa</i> hybridized with various labeled microsatellite-containing oligonucleotides as indicated.

<p>Chromosomes were counterstained with DAPI (blue); microsatellite probes were directly labeled with Cy3 during synthesis (red signals). The cytogenetic marker RAYSI (green) was used to identify Y1 and Y2 chromosomes. The X and Y chromosomes are indicated. The bar indicates 10 µm.</p

The occurrence of selected microsatellites near transposable elements.

<p>The occurrence of selected microsatellites in the 50 bp upstream (positions 1–50) and 50 bp downstream (positions 51–100) of transposable elements insertion sites (indicated by arrow) in DNA transposons (A), LTR retrotransposons (B), LINE (C) and SINE (D) in human. The observed distributions of microsatellites in the vicinity ofTEs are in red, distributions of microsatellites in a vicinity of random loci from our simulations are in blue (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045519#s4" target="_blank">Materials and Methods</a>). Proportion of TEs (%)/proportion of random loci (%) that have at least one microsatellite array in their vicinity are indicated for each TE group.</p

A model depicting the dynamism of microsatellites and transposable elements (TEs) on the evolving Y chromosome.

<p>The first event is an expansion of microsatellite arrays (red boxes) on a young Y chromosome. Then TEs (blue boxes) are inserted (black arrows) into microsatellite loci. Later ectopic recombination between homologous TEs results in deletions of intervening regions containing microsatellites. Finally, an old Y chromosome contains only short microsatellite loci (interrupted by TEs) and a large number of TEs.</p