Microsatellites (also known as short tandem repeats) are repetitive DNA elements usually found in non-coding regions of the genome. They have high mutation rates, and therefore are frequently highly polymorphic. Variations in the number of repetitions generate different alleles. This makes them appropriate molecular markers for population genetics and molecular ecology projects.
At AllGenetics, we use high-throughput sequencing to obtain primer pairs which amplify polymorphic microsatellite loci in your study species. Genomic DNA is used to generate genomic libraries. We usually enrich these libraries with 4 to 6 different microsatellite motifs. However, we can customise the number of motifs to your needs. We obtain thousands of microsatellite-containing reads by using high-throughput sequencing. Our bionformaticians use these reads for primer design. The primers obtained are multiplexed and tested for polymorphism in a number of individuals from different populations.
Our microsatellite development projects are divided into 3 steps. We can carry out the entire project or only the parts you need.
Deliverables include your results, the raw data generated (which will be delivered through our server), and a summary of the methods followed.
A research team from the Universidade da Coruña was interested in developing polymorphic microsatellite markers in a marine crustacean species. They were to be used in a wide population genetic survey.
They gave us ethanol-preserved individuals which our technical team extracted DNA from. A microsatellite-enriched genomic library was constructed and sequenced in a HTS platform. Reads were filtered according to quality parameters. Then, those containing appropriate microsatellite motifs were selected for primer design. One hundred primer pairs were multiplexed and tested in 15 individuals from different populations. Our bioinformaticians analysed the electropherograms in order to select those primer pairs amplifying polymorphic regions.
We delivered a comprehensive methodological report, together with all the sequence reads, primers, and labelled probes that had been generated. The researchers were then able to begin the genotyping of crustacean populations.