Microsatellite loci for Symbiodinium A3 Identified using next-generation sequencing

Microsatellites, or simple sequence repeats (SSRs), are molecular markers that can be readily investigated for population genetic studies. Microsatellites contain tandem repeats of 1-6 bases and are usually highly polymorphic, displaying a large number of alleles. The high degree of polymorphism makes microsatellites an ideal tool for studying gene-flow.

A recent study by Pinzon et al. developed ten polymorphic microsatellite loci for a common algae (Symbiodinium fitti, type A3) to study coral-algal symbioses. For this study, genomic DNA from three cultured strains of S. fitti were extracted and purified. Two different methods were employed to identify microsatellite loci with di-, tri-, and tetranucleotide motifs: i) Roche 454 sequencing; and ii) standard clone library (TA cloning) amplified and cycle sequenced using the ABI’s Big Dye Terminator Kit. For the Roche 454 sequencing, libraries were prepared from only 50 ng of double-stranded DNA using the Nextera™ DNA Sample Prep Kit (FLX Titanium-compatible), and sequenced on the 454 GS-FLX sequencer. The sequencing results helped the authors identify three to eight alleles for each haploid locus, with <95% of the samples possessing a single, symbiont, multilocus genotype (MLG).

The study demonstrates the utility of next-generation sequencing (NGS), especially with limited amounts of DNA. As shown in this study, NGS can be used to identify population genetic markers, which can help scientists better understand intraspecific and interspecific gene flow and population genetic structure.

Pinzón, J. et al. (2010). Microsatellite loci for Symbiodinium A3 (S. fitti) a common algal symbiont among Caribbean Acropora (stony corals) and Indo-Pacific giant clams (Tridacna) Conservation Genetics Resources, 3 (1), 45-47 DOI: 10.1007/s12686-010-9283-5