Home > Explore Data & Reports > Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline

Citation:

Fernandez-Silva, I., J. Whitney, B. Wainwright, K.R. Andrews, H. Ylitalo-Ward, B.W. Bowen, R.J. Toonen, E. Goetze, and S.A. Karl. 2013. Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. PLoS ONE, 8(2):e55990. https://doi.org/10.1371/journal.pone.0055990

Data/Report Type:

Sponsored Research

Description

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.

Note to readers with disabilities: Some scientific publications linked from this website may not conform to Section 508 accessibility standards due to the complexity of the information being presented. If you need assistance accessing this electronic content, please contact the lead/corresponding author, Primary Contact, or nccos.webcontent@noaa.gov.

Explore Similar Data/Reports

About NCCOS

NCCOS delivers ecosystem science solutions for stewardship of the nation’s ocean and coastal resources to sustain thriving coastal communities and economies.

Stay Connected

Sign up for our quarterly newsletter or view our archives.

Follow us on Social

Listen to our Podcast

Check our our new podcast "Coastal Conversations"