Photomicrographs of 2 of the animals discussed here.

<p>The bdelloid rotifer <i>Rotaria macrura</i> (top) and the tardigrade <i>Hypsibius dujardini</i> (bottom). Image credits: Michael Plewka and Kazuharu Arakawa.</p

Variability is correlated with increasing repeat length, increasing purity, and decreasing unit size.

<p>Correlations were made using genotypes of repeats (2mers to 5mers) that were derived from genomes sequenced with a read length of at least 75 bases. Data points were plotted at each reference length bin interval that contained at least 25 repeats. The mean number of alleles (A) positively correlated with purity and (B) negatively correlated with unit size.</p

Changes in repeat length typically occur in the form of insertions and deletions of whole repeated units.

<p>The plotted dataset consisted of repeats that were at least 90% pure, with a minimum reference repeat length of 13, 20, 23, and 27 bases for (A) 2mers, (B) 3mers, (C) 4mers, and (D) 5mers, respectively. Genotypes were determined if there were at least two scorable reads and a read was scored if it spanned the repeat region with 3 or more matching flank bases on either side of the repeat.</p

The tendency for differences in repeat length to occur in the form of insertions and deletions of whole repeated units increases with repeat tract length.

<p>The percent in-phase values of uninterrupted 2mer, 3mer, 4mer, and 5mer repeats approached a plateau at repeat lengths of 13, 20, 23, and 27 bases respectively, where length-changes are close to 100% in-phase. Genotypes for pure repeats were determined in all the DGRP lines if there were at least two scorable reads and a read was scored if it spanned the repeat region with 3 or more matching flank bases on either side of the repeat.</p

The completeness and internal concordance of microsatellite repeat genotypes in the Drosophila genome.

<p>The plotted values are the mean (A) completeness (fraction of repeats with at least two reads passing filtering criteria) and (B) concordance for the genomes in the DGRP panel, grouped by read length. Data have been smoothed for clarity (unweighted mean with window size ±2 bases). For this initial analysis, only a single matching base on each side of the repeat was required for a read to be scored.</p

The distributions of repeat lengths in Drosophila and human genomes.

<p>The heights of the bars indicate the relative abundance of repeats at various lengths in Drosophila (black) and human (gray) genomes. The solid portions indicate the fraction of (A) all repeats 80% pure or greater, and (B) pure repeats that can be genotyped based on observed completeness using reads that are at least 100 bases.</p

Repeats of shorter unit length are more difficult to sequence.

<p>The plotted values are the mean (A) completeness (fraction of repeats with at least two reads passing filtering criteria) and (B) concordance for the genomes in the DGRP panel. Data have been smoothed for clarity (unweighted mean with window size ±2 bases).</p

Number of identified microsatellites and their association with repetitive elements by chromosome.

a<p>Number (%) of microsatellites within 20 bases of a large repetitive element.</p

Analysis of discordant genotypes in genomes sequenced with two different read lengths reveals that short reads exhibit a bias towards shorter alleles.

<p>The difference between the inferred genotypes and the corresponding reference repeat length was tallied for 6,908 (out of 390,873) repeats for which different genotypes were obtained in the same inbred line from 45 base (open bars) versus 75 base (solid bars) reads. Permutation testing (1000 trials) indicates that the bias toward shorter alleles evident in the 45 base libraries is significant (for clarity, only the upper half of 95% confidence intervals are shown).</p