Data from: Repetitive flanking sequences challenge SSR marker development: a case study in the lepidopteran Melanargia galathea

Microsatellite DNA families (MDF) are stretches of DNA that share similar
or identical sequences beside nuclear simple-sequence repeat (nSSR)
motifs, potentially causing problems during nSSR marker development.
Primers positioned within MDFs can bind several times within the genome
and might result in multiple banding patterns. It is therefore common
practice to exclude MDF loci in the course of marker development. Here, we
propose an approach to deal with multiple primer binding sites by
purposefully positioning primers within the detected repetitive element.
We developed a new protocol to determine the family type and the primer
position in relation to MDFs using the software packages RepARK and
RepeatMasker together with an in-house R script. We re-evaluated newly
developed nSSR markers for the lepidopteran Marbled White (Melanargia
galathea) and explored the implications of our results with regard to
published data sets of the butterfly Ephydryas aurinia, the grasshopper
Stethophyma grossum, the conifer Pinus cembra, and the crucifer Arabis
alpina. For M. galathea, we show that it is not only possible to develop
reliable nSSR markers for MDF loci, but even to benefit from their
presence in some cases: We used one unlabeled primer, successfully binding
within an MDF, for two different loci in a multiplex PCR, combining this
family primer with uniquely binding and fluorescently labeled primers
outside of MDFs, respectively. As MDFs are abundant in many taxa, we
propose to consider these during nSSR marker development in taxa
concerned. Our new approach might help in reducing the number of tested
primers during nSSR marker development.