Using next-generation sequencing to identify SSRs in de novo sequences

Simple sequence repeats (or microsatellites) are tandem DNA repeats that are highly polymorphic, making them ideal for population studies among arthropod groups. However, SSRs remain time-consuming and expensive to develop de novo, and in many cases, it is preferable to use a reference source of SSRs as a guide for developing homologous markers across related taxa. Here, using Illumina Solexa sequencing, we demonstrate a novel approach to locate SSRs in a non-model organism. Because of their low complexity, Solexa contigs rarely span SSRs. However, by mapping the de novo Solexa assemblies to reference genomes in which SSRs have been previously identified, regions of disproportionately low coverage can reveal the likelihood of the presence or absence of SSRs. SSR-targeted mapping then greatly enriches the pool of candidate loci for development, while providing exact information on flanking sequences for primer development. We tested this hypothesis with the gall midge Asteromyia carbonifera, which is a distant relative of the Hessian fly (Mayetiola destructor), a well-characterized pest with abundant genomic resources. This approach will provide a cheap and efficient method for identifying SSRs for population level studies.