Domain-Level Differences in Microsatellite Distribution and Content Result from Different Relative Rates of Insertion and Deletion Mutations

Abstract

Microsatellites (short tandem polynucleotide repeats) are found throughout eukaryotic genomes at frequencies many orders of magnitude higher than the frequencies predicted to occur by chance. Most of these microsatellites appear to have evolved in a generally neutral manner. In contrast, microsatellites are generally absent from bacterial genomes except in locations where they provide adaptive functional variability, and these appear to have evolved under selection. We demonstrate a mutational bias towards deletion (repeat contraction) in a native chromosomal microsatellite of the bacterium Mycoplasma gallisepticum, through the collection and analysis of independent mutations in the absence of natural selection. Using this and similar existing data from two other bacterial species and four eukaryotic species, we find strong evidence that deletion biases resulting in repeat contraction are common in bacteria, while eukaryotic microsatellites generally experience unbiased mutation or a bias towards insertion (repeat expansion). This difference in mutational bias suggests that eukaryotic microsatellites should generally expand wherever selection does not exclude them, whereas bacterial microsatellites should be driven to extinction by mutational pressure wherever they are not maintained by selection. This is consistent with observed bacterial and eukaryotic microsatellite distributions. Hence, mutational biases that differ between eukaryotes and bacteria can account for many of the observed differences in microsatellite DNA content and distribution found in these two groups of organisms.

Inter- and Intra-Strain Variability of Tandem Repeats in Mycoplasma Pneumoniae Based on Next-Generation Sequencing Data

“…Including all loci showing heterogeneous repeat copy numbers, the overall rate of repeat deletions was significantly higher than that of repeat insertions (60.6 vs 39.4%; p = 0.0276; Supplementary Table 9), in agreement with previous reports [44]. In addition, in two loci (Mpn108b and Mpn111) almost all alleles with >10 repeats showed extensive intrastrain heterogeneity in the repeat copy number in sharp contrast to the high homogeneity in alleles with <10 repeats (Table 2), consistent with the notion that higher copy number alleles are more unstable than lower copy number alleles [45].…”

Identification and validation of novel EST-SSR markers in olives

“…In CDSs, trinucleotide motifs were predominant (33 %). This result is in accordance with previous studies, which showed that selection against frameshift mutations limits nontriplet SSRs expansion in CDS regions (Metzgar et al, 2002).…”

A multiplex PCR for detection of Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, and Bordetella pertussis in clinical specimens

“…Primers will not contain G/C runs of >4 bp (G/C bases will be as evenly spaced as possible), and primers will not contain repetitive sequences (AAAAA, GAGAGA, etc). It is especially important to avoid repetitive sequences because they are far more common in eukaryotic genomes than sequences of greater complexity [38], and will therefore be more likely to misanneal to host sequences.…”