Microsatellites- effects of repeat motif
In this study we evaluated four ‘simple’ repeat motif markers and a single ‘complex’ repeat motif. The GLSA-12 marker was the only ‘complex’ motif, characterized by a repeat region that was interrupted multiple times, and contained three regions of dinucleotide elements, see Table 2. All other microsatellites included dinucleotide repeats which were not interrupted. Based on the PCR replicate results (summarized in Appendix 1) the GLSA-12 locus performed the same as the other medium length microsatellite locus for all museum specimens, and failed a single PCR replicate of the HSU 8180 tissue sample (when repeated a third time this sample produced a matching genotype). Across all samples GLSA-12 amplified successfully 36.3% of the time as compared with 34% for the other medium length marker (GLSA-22). When evaluating the resulting genotypes, GLSA-12 recovered four out of seven genotypes versus five out of seven genotypes for GLSA-22 (see Table 4). The difference between GLSA-12 and GLSA-22 was one LQMS (MVZ 2088) which was amplified in GLSA-22. The complex motif, however, was not recovered as previously published in G. sabrinus (Kiesow et al., 2011).The published motif, (GT)5A(TG)3TTT(GT)5 varied from what we recovered here: (GT)13TT(GT)5 (HSU 1836) and (GT)11TT(GT)5 (HSU 8180). Overall, it does not appear that the complexity of the repeat motif influenced the rate of genotyping success in these samples, however we have limited data to conclude if the complexity affected genotyping rates.