Why you should be using multiple genomes when searching for new microsatellite markers

Microsatellites markers are amongst the real workhorses of molecular ecology techniques. But what to do if markers are not already available for your species? Developing markers in a new species can be a slow and expensive process, however a new bioinformatics tool has been released which can make marker testing much faster, and cheaper.

Developed by PhD student Graeme Fox, this new tool, MiMi (Multi-individual Microsatellite identification), allows the information from multiple genomes to be used in the design process, meaning that many tests of a marker can be performed in silico, rather than requiring long hours in the lab. Our algorithm finds the microsatellites in several individuals and by making comparisons in their sequences, automatically selects variable loci, with highly conserved PCR primers – giving your new markers the best possible chance of being successful in the lab!

We tested MiMi during the design of new markers in the Green Sea Urchin (P. miliaris) and found that we were able to boost the rate at which we found good markers by 52%. Graeme Fox says that one of the best things about this tool is that it could “save your lab around 50% in staff costs, and 20% in reagent costs; leaving you with more time and resources to answer the real questions!”

You can see the paper here, download it here, and access the MiMi script here.