A family study to examine clonal diversity in unisexual salamanders (genus Ambystoma)

Unisexual Ambystoma are the oldest known unisexual vertebrates and comprise a lineage of eastern North American all female salamanders that reproduce by stealing sperm from as many as five normally bisexual congeneric species. The sperm may be used to only stimulate egg development by gynogenesis but can be incorporated in the zygote to elevate the ploidy level or to replace one of the female’s haploid genomes. This flexible and unique reproductive system, termed kleptogenesis, is investigated using a microsatellite examination of 988 offspring from 14 unisexual mothers. All mothers produced clonal and ploidy-elevated offspring. Genome replacement and multiple paternity are confirmed for the first time in unisexual Ambystoma. Microsatellite mutations were found in all five microsatellite loci and the estimated microsatellite mutation rate varied by locus and by genome. Clonal variation is attributed to the inclusion of sperm donors’ haploid genomes for ploidy elevation, genome replacement, mutations, and natural selection.

Comprehensive Analysis of Indels in Whole-genome Microsatellite Regions and Microsatellite Instability across 21 Cancer Types

Microsatellites are repeats of 1-6bp units and ∼10 million microsatellites have been identified across the human genome. Microsatellites are vulnerable to DNA mismatch errors, and have thus been used to detect cancers with mismatch repair deficiency. To reveal the mutational landscape of the microsatellite repeat regions at the genome level, we analyzed approximately 20.1 billion microsatellites in 2,717 whole genomes of pan-cancer samples across 21 tissue types. Firstly, we developed a new insertion and deletion caller (MIMcall) that takes into consideration the error patterns of different types of microsatellites. Among the 2,717 pan-cancer samples, our analysis identified 31 samples, including colorectal, uterus, and stomach cancers, with higher microsatellite mutation rate (≥ 0.03), which we defined as microsatellite instability (MSI) cancers in genome-wide level. Next, we found 20 highly-mutated microsatellites that can be used to detect MSI cancers with high sensitivity. Third, we found that replication timing and DNA shape were significantly associated with mutation rates of the microsatellites. Analysis of germline variation of the microsatellites suggested that the amount of germline variations and somatic mutation rates were correlated. Lastly, analysis of mutations in mismatch repair genes showed that somatic SNVs and short indels had larger functional impact than germline mutations and structural variations. Our analysis provides a comprehensive picture of mutations in the microsatellite regions, and reveals possible causes of mutations, as well as provides a useful marker set for MSI detection.

Heterozygosity increases microsatellite mutation rate

Whole genome sequencing of families of Arabidopsis has recently lent strong support to the heterozygote instability (HI) hypothesis that heterozygosity locally increases mutation rate. However, there is an important theoretical difference between the impact on base substitutions, where mutation rate increases in regions surrounding a heterozygous site, and the impact of HI on sequences such as microsatellites, where mutations are likely to occur at the heterozygous site itself. At microsatellite loci, HI should create a positive feedback loop, with heterozygosity and mutation rate mutually increasing each other. Direct support for HI acting on microsatellites is limited and contradictory. I therefore analysed AC microsatellites in 1163 genome sequences from the 1000 genomes project. I used the presence of rare alleles, which are likely to be very recent in origin, as a surrogate measure of mutation rate. I show that rare alleles are more likely to occur at locus-population combinations with higher heterozygosity even when all populations carry exactly the same number of alleles.

Temperature, stress and spontaneous mutation in Caenorhabditis briggsae and Caenorhabditis elegans

Mutation rate often increases with environmental temperature, but establishing causality is complicated. Asymmetry between physiological stress and deviation from the optimal temperature means that temperature and stress are often confounded. We allowed mutations to accumulate in two species of Caenorhabditis for approximately 100 generations at 18°C and for approximately 165 generations at 26°C; 26°C is stressful for Caenorhabditis elegans but not for Caenorhabditis briggsae . We report mutation rates at a set of microsatellite loci and estimates of the per-generation decay of fitness (Δ M w ), the genomic mutation rate for fitness ( U ) and the average effect of a new mutation ( E [ a ]), assayed at both temperatures. In C. elegans , the microsatellite mutation rate is significantly greater at 26°C than at 18°C whereas in C. briggsae there is only a slight, non-significant increase in mutation rate at 26°C, consistent with stress-dependent mutation in C. elegans . The fitness data from both species qualitatively reinforce the microsatellite results. The fitness results of C. elegans are potentially complicated by selection but also suggest temperature-dependent mutation; the difference between the two species suggests that physiological stress plays a significant role in the mutational process.