Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans

Abstract

We report the draft genome sequences of Geomyces pannorum sensu lato and Geomyces (Pseudogymnoascus) destructans. G. pannorum has a larger proteome than G. destructans, containing more proteins with ascribed enzymatic functions. This dichotomy in the genomes of related psychrophilic fungi is a valuable target for defining their distinct saprobic and pathogenic attributes.

GENOME ANNOUNCEMENT

Geomyces pannorum is a soil-dwelling fungus common in colder parts of the world (1–3). G. pannorum is rarely implicated in the human disease geomycosis, which manifests as skin and nail infections (4–6). Geomyces destructans is the etiologic agent of bat geomycosis or white nose syndrome (WNS) (7, 8). G. destructans is restricted to caves and mines in the United States and Europe (9, 10). G. pannorum sensu lato represents a species complex, while G. destructans was recently reclassified as Pseudogymnoascus destructans (2, 9). As taxonomy is in a state of flux, G. destructans and G. pannorum will be used as the organism names throughout this work. Both fungi are adapted to a psychrophilic range (4° to 15°C) and express enzymes implicated in fungal virulence (1, 3, 8, 11). The study of the biology and pathogenicity of psychrophilic fungi is in its infancy due to a lack of experimental tools. This is also true for other eukaryotes inhabiting colder parts of the earth.

Genomic DNA from G. pannorum M1372 and G. destructans M1379 was obtained by phenol-chloroform extraction of pulverized fungal mycelia. The Illumina HiSeq 2000 was used for 100-base paired-end sequencing. The assemblies were generated using four programs, subsampling 89 million reads for G. pannorum and 88 million reads for G. destructans. Optimal assemblies representing 100× coverage for G. pannorum and 150× coverage for G. destructans were generated with MaSuRCA version 1.9.2 (12). The G. pannorum assembly is 29.47 Mb, with a G+C content of 50.5%, and comprises 856 scaffolds ranging in length from 300 bases to 839 kb (average, 34.4 kb; median, 7.9 kb; N₅₀, 105 kb). G. destructans is 30.49 Mb, with a G+C content of 49.8%, and was assembled into 5,008 scaffolds of length 108 bases to 234 kb (average, 6.1 kb; median, 1.8 kb; N₅₀, 19.2 kb). Fifty-two percent of the G. destructans reference DNA shares similarity with G. pannorum query DNA, with 45% of it being identical. A custom ab initio gene prediction pipeline generated 9,689 G. pannorum proteins and 7,967 G. destructans proteins. The difference in the coding density, which is 48% for G. pannorum and 37% for G. destructans, is attributable to the smaller number of proteins and numerous repeats (25.8% of the genome) in G. destructans than in G. pannorum (5.40% repeats). CEGMA predicted 96.7% of the 458 conserved genes in G. destructans and 98.3% in G. pannorum (13). Functional annotation with BLAST against UniProt (14) and HMM searches against TIGRfams/Pfams (15, 16) yielded Gene Ontology annotations (17) for 62.3% of the G. destructans proteins and 63.1% of the G. pannorum proteins. EC assignments were given to 2,052 G. destructans proteins (25.8%) and 2,734 G. pannorum proteins (28.2%). Thus, G. pannorum contains more proteins than G. destructans, including more with ascribed enzymatic functions. This dichotomy in the genomes of related psychrophilic fungi is a valuable target for defining their distinct saprobic and pathogenic attributes.

Nucleotide sequence accession numbers.

The G. (Pseudogymnoascus) destructans whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AYKP00000000. The version described in this paper is AYKP01000000. The G. pannorum whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AYKR00000000. The version described in this paper is AYKR01000000.