Comparative Genome-Wide Characterization of Microsatellites in Candida albicans and Candida dubliniensis Leading to the Development of Species-Specific Marker

Abstract

Background: Microsatellites or simple sequence repeats (SSR) are related to genomic structure, function, and certain diseases of taxonomically different organisms. Objective: To characterize microsatellites in two closely related Candida species by searching and comparing 1–6 bp nucleotide motifs and utilizing them to develop species-specific markers. Methods: Whole-genome sequence was downloaded from the public domain, microsatellites were mined and analyzed, and primers were synthesized. Results: A total of 15,821 and 7,868 microsatellites, with mono-nucleotides (8,679) and trinucleotides (3,156) as most frequent microsatellites, were mined in Candida dubliniensis and Candida albicans, respectively. Chromosome size was found positively correlated with microsatellite number in both the species, whereas it was negatively correlated with the relative abundance and density of microsatellites. A number of unique motifs were also found in both the species. Overall, microsatellite frequencies of each chromosome in C. dubliniensis were higher than in C. albicans. Conclusion: The features of microsatellite distribution in the two species’ genomes revealed that it is probably not conserved in the genus Candida. Data generated in this article could be used for comparative genome mapping and understanding the distribution of microsatellites and genome structure between these closely related and phenotypically misidentified species and may provide a foundation for the development of a new set of species-specific microsatellite markers. Here, we also report a novel microsatellite-based marker for C. dubliniensis-specific identification.