Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline

Area of Science:

• Genetics
• Bioinformatics
• Molecular Biology

Background:

• Microsatellites are crucial markers for population genetics.
• Next-generation pyrosequencing accelerates microsatellite discovery but primer validation is costly.
• Current in silico methods for microsatellite detection have limitations.

Purpose of the Study:

• To develop and validate a bioinformatic pipeline for pre-screening microsatellite loci.
• To improve the efficiency and success rate of primer selection for microsatellite analysis.
• To reduce the time and cost associated with laboratory validation of microsatellite markers.

Main Methods:

• Developed a bioinformatic pipeline for screening microsatellite loci.
• Emphasized sequence quality control and screening against repetitive elements using specialized databases.
• Validated the pipeline using Yellowstripe Goatfish (Mulloidichthys flavolineatus) and Pleuromamma xiphias.

Main Results:

• The developed pipeline demonstrated a higher success rate for selected primers compared to previous in silico methods.
• Successfully identified and selected microsatellite loci in nine additional species, including fish, sea stars, copepods, and octopuses.
• The bioinformatic approach significantly reduces the workload for laboratory testing.

Conclusions:

• Bioinformatic pre-screening of microsatellite loci is an effective strategy to enhance primer selection efficiency.
• This approach offers a cost-effective and time-saving solution for population genetic research.
• The pipeline is applicable across diverse taxa, facilitating broader use in genetic studies.