Hybrid Genome Sequence of Cryptococcus neoformans of Indian origin and comparative genome analysis

Abstract

ObjectivesThe Indian isolate of Cryptococcus neoformans underwent complete genome sequencing to elucidate its genomic architecture and functional characteristics. Furthermore, this study aimed to comprehensively characterize the virulence factors (virulome), antibiotic resistance genes (resistome), and the pan-genome of C. neoformans spp. through a comparative genomic analysis, providing insights into the genetic diversity and evolutionary relationships among strains. MethodsThe genomic data of a clinical strain of C. neoformans was assembled and annotated by MaSuRCA5 and Braker tool. Along with this, the assembled genomic data of the 11 strains were retrieved from NCBI datasets. The comparative virulome, resistome, phylogeny and of the 12 C. neoformans genomes were analyzed using DFVF, AFRbase, BLAST, CLUSTAL Omega, MEGAX, and Orthovenn3, respectively. ResultsThe sequenced isolate was identified as a member of the Cryptococcus neoformans var. grubii subspecies. Notably, virulence-related genes comprise approximately 4.8% of the total genome. A comparative genomic analysis of 12 study genomes revealed variations in virulence patterns, including differences in melanization, immune evasion, blood-brain barrier evasion, transcriptional regulation, and oxidative stress response. The phylogenetic study using MLST and orthologous clusters categorized the subspecies grubii and neoformans in different clades. Pan-genome analysis showed that 73.6% of orthologous gene clusters and 77.72% of orthologous proteins were conserved across all 12 study genomes, indicating a shared core genome. Furthermore, the evolutionary relatedness study of the pan-genome revealed gene expansion and contraction events among the study strains. ConclusionThis pioneering study presents the first comprehensive genomic and comparative genomic analysis of Cryptococcus sp., incorporating data on virulence genes, antibiotic resistance, and pan-genome dynamics. Key findings reveal that strains Cn, H99, and JEC21 harbor crucial virulence genes associated with infection severity. While all study strains possess genes promoting antifungal resistance (AFR), most lack specific single nucleotide polymorphisms defining AFR. Consistent with pan-genome analysis, our results show significant gene expansion and contraction events in these strains. This study underscores the importance of bioinformatic tools for efficient whole-genome analysis and large-scale comparative genomics research.