Elucidation of SSR polymorphism in human pathogenic fungi Cryptococcus neoformans with focus on isolate-specific marker generation and genetic diversity assessment

Abstract

This work aimed to conduct a comparative analysis of the occurrence, relative density (RD) and abundance (RA) of simple sequence repeats (SSRs), within the genomic and transcriptomic sequences of four different isolates of Cryptococcus neoformans. Among the whole genome sequences, it was observed that the C. neoformans isolate JEC21 exhibited the most elevated RA (165.3) and RD (2471.8) of SSRs. Conversely, among the transcriptome sequences, the C. neoformans isolate KN99 displayed the greatest RA (145.5) of SSRs. Among the classes of SSRs, trinucleotide repeats exhibited a higher prevalence in both the genomic sequences (50%) and transcriptome sequences (65%) over other repeats. Motif conservation analysis among the isolates demonstrated that 41.1% of motifs were conserved among the isolates of C. neoformans. The study also found unique motifs that could potentially serve as molecular probes for the purpose of isolate identification. A total of 8117 primers were created for the isolates of Cryptococcus to enrich it with genomic resources. The genomic resources created in this study have the potential to aid in the diversity analysis and the creation of markers specific to individual isolates.