The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans

Abstract

Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.

Fig. 1

The C. neoformans JEC21 genome with each chromosome represented as a colored bar. Specific features are pseudocolored, from red (high density) to deep blue (low density) and plotted on a log scale. These include the density of genes, transposons, expressed sequence tags (ESTs), and predicted SNPs and indels. Candidate centromeric regions and the MAT locus are represented as red bars and a blue bar, respectively. The location of the rDNA repeat is represented by a green bar.

Fig. 2

Gene structures that display evidence for both alternative splicing and natural in cis antisense transcripts based on JEC21 cDNA alignments to the genome sequence. Colored boxes represent exonic regions. Each gene structure represents an alternative spliced form. The black line represents the genomic sequence.