A simple method to generate PCR-RFLP typing profiles from DNA sequences in Toxoplasma gondii

Multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) has been widely used to genotype microorganisms. Accumulation of data generated by this method has helped to reveal genetic diversity, population structure and transmission of many microbial pathogens. Advances in DNA sequencing technologies have made it possible to identify microorganisms by multilocus sequencing typing (MLST) or whole genome sequence typing (WGST) to reach high resolution of identification. While MLST and WGST are gradually replacing PCR-RFLP for genotyping, invaluable databases generated by the latter may not be easily linked to datasets generated by sequencing based methods. In addition, DNA sequences corresponding to PCR-RFLP markers are often deposited in public domains but not fully explored to infer the RFLP profile. To alleviate this problem, we developed a simple protocol that can generate PCR-RFLP profiles from DNA sequence data, therefore facilitating the integration of data generated by different typing methods. Here we used the protozoan parasite Toxoplasma gondii as an example to bridge different typing methods.