A Landscape of the Genomic Structure of Cryptococcus neoformans in Colombian Isolates

Abstract

Cryptococcus neoformans species complexes are recognized as environmental fungi responsible for lethal meningoencephalitis in immunocompromised individuals. Despite the vast knowledge about the epidemiology and genetic diversity of this fungus in different regions of the world, more studies are necessary to comprehend the genomic profiles across South America, including Colombia, considered to be the second country with the highest number of Cryptococcosis. Here, we sequenced and analyzed the genomic architecture of 29 Colombian C. neoformans isolates and evaluated the phylogenetic relationship of these strains with publicly available C. neoformans genomes. The phylogenomic analysis showed that 97% of the isolates belonged to the VNI molecular type and the presence of sub-lineages and sub-clades. We evidenced a karyotype without changes, a low number of genes with copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs). Additionally, a difference in the number of SNPs between the sub-lineages/sub-clades was observed; some were involved in crucial fungi biological processes. Our study demonstrated the intraspecific divergence of C. neoformans in Colombia. These findings provide evidence that Colombian C. neoformans isolates do not probably require significant structural changes as adaptation mechanisms to the host. To the best of our knowledge, this is the first study to report the whole genome sequence of Colombian C. neoformans isolates.

Keywords: CNV; Cryptococcus neoformans; SNP; whole genome sequencing.

Figure 1

Phylogenetic relationship among the Cryptococcus genomes. (A) The figure represents the phylogenomic inference based on whole genome SNP alignments for the 611 genomic sequences analyzed in this study. The red dots represent the 29 Colombian genomes. (B) Phylogenetic networks constructed in SplitsTree 5, based on SNP alignments for 611 genomes analyzed. C. neoformans strain H99 was used as the reference genome, and C. gattii WM276 as an outgroup.

Figure 2

Phylogenetic analysis of Colombian Cryptococcus neoformans genomes. (A) Phylogenomic inference based on SNP alignments for the 29 Colombian genomic sequences included in this study. Black dots represent well-supported nodes (bootstrap ≥ 90). (B) Phylogenetic networks constructed in SplitsTree 5, based on SNP alignments for 29 Colombian genomes. The bottom figure represents the magnification of cluster 3 (VNI) to visualize the VNI sub-lineages. Genomes representatives for each of the four molecular types previously described for C. neoformans were included: VNI (ERR1395134), VNII (ERR1395124), VNIV (ERR1520667), and VNB (ERR1520666).

Figure 3

Evaluation of genes with copy number variation (CNV) across VNIa and VNIb sub-lineages. The table shows the genes with CNV shared between the genomes belonging to VNIa (A) and VNIb (B). On the right, the Gene Ontology enrichment analysis to functional categories (molecular, biological, and cellular) for each sub-lineage (VNIa and VNIb).

Figure 4

Evaluation of genes with copy number variation (CNV) shared between the 29 Colombian Cryptococcus neoformans genomes. (A) The genes with CNV were shared between the 29 isolates included in the study. (B) Gene Ontology enrichment analysis to functional categories (molecular, biological, and cellular).

Figure 5

The landscape of SNPs identified in the 29 Colombian Cryptococcus neoformans genomes. (A) The figure describes the number of SNPs identified per chromosome, with a potential effect on gene function, in each genome analyzed, as well as the number of shared SNPs in the VNI sub-lineage (VNIa and VNIb) and the number of shared SNPs between the 29 genomes included in the study. (B) The density of SNPs in each of the 29 genomes was analyzed.