Identification of lineage-associated polymorphisms in the ROP18 3' flanking region and development of molecular assays for differentiation of Toxoplasma gondii lineages.

BACKGROUND: Toxoplasma gondii (T. gondii) exhibits substantial genetic diversity, and different parasite lineages are associated with distinct epidemiological distributions and biological characteristics. Accurate molecular characterization of T. gondii strains is important for understanding parasite population structure and transmission patterns. However, existing genotyping approaches often require multiple loci, extensive experimental procedures, or complex data analysis. Therefore, simplified and reliable molecular markers for rapid lineage differentiation are still needed. METHODS: In this study, comparative genomic analysis was performed using representative T. gondii strains with well-defined genetic backgrounds and virulence phenotypes. The ROP18 genomic region, including partial genomic sequences, 5' flanking regions, coding sequence (CDS), and 3' flanking regions, was analyzed to identify informative polymorphic signatures. A short conserved sequence region containing lineage-associated polymorphic sites was identified within the ROP18 3' flanking region. Based on these sequence signatures, HRM-PCR and TaqMan MGB probe-based real-time PCR assays were developed and evaluated using plasmid standards and representative T. gondii genomic DNA samples. RESULTS: Phylogenetic analyses based on different ROP18 genomic regions demonstrated distinct clustering patterns among analyzed strains. Although the ROP18 3' flanking region was highly conserved, a short conserved sequence region containing informative polymorphic sites was identified, and the combination of these sites generated three distinct lineage-associated ROP18 patterns. Analysis of publicly available genomic datasets further demonstrated that individual strains contained one of these defined patterns rather than multiple patterns simultaneously. The developed HRM-PCR assay successfully discriminated the three ROP18-associated patterns based on distinct melting profiles with good reproducibility. Furthermore, the TaqMan MGB probe-based assay enabled specific identification of different ROP18-associated patterns through defined probe-recognition combinations and showed good analytical performance. CONCLUSION: This study identifies novel lineage-associated molecular signatures within the ROP18 3' flanking region and establishes complementary HRM-PCR and TaqMan MGB probe-based approaches for rapid molecular differentiation of T. gondii strains. These findings highlight the potential of conserved non-coding regions adjacent to functionally important genes as informative targets for parasite genotyping and provide a practical complementary tool for epidemiological surveillance and strain characterization.