Characterization of simple sequence repeats (SSRs) in Cryptococcus species isolated from soil samples in Ogun State, Nigeria

Cryptococcus species are opportunistic fungal pathogens responsible for severe infections, particularly in immunocompromised individuals. Their genomic plasticity contributes to adaptation, virulence, and antifungal resistance. Simple sequence repeats (SSRs) are useful molecular markers for investigating genetic diversity and evolutionary patterns. However, SSR-based analyses of Cryptococcus isolates in Nigeria remain limited, hindering a comprehensive understanding of local strain diversity and adaptation. This study aimed to evaluate the occurrence, distribution, motif composition, and relative abundance of SSRs in partial genomic sequences of Cryptococcus species isolated from soil samples in Ogun State, Nigeria. Previously isolated Cryptococcus strains were sequenced and analyzed for GC content and SSR characteristics, including SSR occurrence, relative abundance (RA), and relative density (RD). Primer pairs were subsequently designed around the identified SSR regions. A total of 6–22 SSRs were identified per isolate, with GC content ranging from 37% to 46%. No consistent relationship was observed between partial genomic sequence length, GC content, and SSR frequency. Notably, isolates SE3 and SG8, which had the shortest sequences, exhibited the highest SSR relative abundance and density. Isolates with both the lowest and highest GC content also exhibited similarly high SSR abundance. Dinucleotide repeats were the most prevalent motif class (46.2%), followed by trinucleotide (38.5%) and tetranucleotide (15.3%) repeats. Although SSRs were distributed across all partial genomic sequences, motif conservation was low, with only one motif, (TC)n, common to all isolates. Putatively functionally relevant motifs, including (GAA)n, as well as isolate-specific motifs, were also identified. In total, seven SSR primer pairs were designed, five of which were unique to individual isolates. These findings provide insights into the sequence characteristics and distribution patterns of SSRs in Cryptococcus species and provide potential molecular tools for future studies of fungal population genetics, epidemiology, and evolutionary patterns.