Comparative Analysis of Clinical and Environmental Strains of Exophiala spinifera by Long-Reads Sequencing and RNAseq Reveal Adaptive Strategies

Abstract

Exophiala spinifera, a capsule-producing black yeast, is overrepresented as agent of disseminated infection in humans with inherited dysfunction of the CARD9 gene. In a review of published caspase recruitment domain-containing protein 9 (CARD9) deficiency cases, black fungi were linked to mutations other than those prevalent in yeast and dermatophyte cases, and were found to respond to a larger panel of cytokines. Here, we sequenced and annotated the genomes of BMU 08022 from a patient with CARD9 deficiency and two environmental strains, BMU 00051 and BMU 00047. We performed genomic and transcriptomic analysis for these isolates including published black yeasts genomes, using a combination of long-read (PACBIO) and short-read (Illumina) sequencing technologies with a hybrid assembly strategy. We identified the virulence factors, fitness, and the major genetic and gene expression differences between the strains with RNAseq technology. Genome assembly reached sub-chromosome level with between 12,043 and 12,130 predicted genes. The number of indels identified in the clinical strain was higher than observed in environmental strains. We identify a relatively large core genome of 9,887 genes. Moreover, substantial syntenic rearrangements of scaffolds I and III in the CARD9-related isolate were detected. Seventeen gene clusters were involved in the production of secondary metabolites. PKS-cluster 17 was consistently found to be absent in the clinical strain. Comparative transcriptome analysis demonstrated that 16 single-copy genes were significantly differentially expressed upon incubation in brain-heart infusion broth vs. Sabouraud glucose broth. Most of the single-copy genes upregulated with Brain Heart Infusion (BHI) were transporters. There were 48 unique genes differentially expressed exclusively to the clinical strain in two different media, including genes from various metabolic processes and transcriptional regulation. Up-regulated genes in the clinical strain with Gene Ontology (GO) enrichment are mainly involved in transmembrane transport,

Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family

“…In addition, we successfully identified the mitochondrial genome with a size of 26,874 bp ( Table 2 ). The assembly size agrees with the size observed in other strains of this genus (20~38 Mb) [ 16 , 36 ]; additionally, the assembly’s completeness and lack of duplicated BUSCO genes strongly suggest that this is an haploid genome version with no evidence of contamination. The small number of fragmented or missing genes within the assembly indicates that it is a valuable resource for gene prediction and functional annotation efforts, with minimal loss of integrity.…”

“…Mb) [16,36]; additionally, the assembly's completeness and lack of duplicated BUSCO genes strongly suggest that this is an haploid genome version with no evidence of contamination.…”

Fatal dermatophytic pseudomycetoma in a patient with non-HIV CD4 lymphocytopenia

“…The pseudomycetomatous type of dermatophytosis is mainly observed in patients with underlying disorders, particularly following solid organ transplantation (SOT), but some cases were observed in apparently healthy individuals. In the past two decades, several inherited immune disorders have been discovered, of which mutations in the caspase recruitment protein domain 9 ( CARD9 ) is particularly significant for fungi: dermatophytes are one of the main groups emerging with this disorder [ 8 , 9 ]. Lanternier et al [ 10 ] suggested that all dermatophyte infections with this type of clinical course and where the host was reported as otherwise appearing healthy, actually had a non-diagnosed CARD9 disorder.…”