title: Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.
abstract: Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.
authors: Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, United States of America. iriafernandezsilva@gmail.com
authors: Iria
authors: I
authors: Fernandez-Silva
authors: Jonathan
authors: J
authors: Whitney
authors: Benjamin
authors: B
authors: Wainwright
authors: Kimberly R
authors: KR
authors: Andrews
authors: Heather
authors: H
authors: Ylitalo-Ward
authors: Brian W
authors: BW
authors: Bowen
authors: Robert J
authors: RJ
authors: Toonen
authors: Erica
authors: E
authors: Goetze
authors: Stephen A
authors: SA
authors: Karl
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030541:Databases, Genetic; D004463:Ecology; D005399:Fishes / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics*; D017421:Sequence Analysis; D013215:Starfish / Q000235:genetics