Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade

• Published in: BMC genomics Vol. 23; no. 1; pp. 506 - 12
• Main Authors: Du, Weian, Giosa, Domenico, Wei, Junkang, Giuffrè, Letterio, Shi, Ge, El Aamri, Lamya, D'Alessandro, Enrico, Hafidi, Majida, de Hoog, Sybren, Romeo, Orazio, Huang, Huaiqiu
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12.07.2022; BioMed Central; BMC
• Subjects: Analysis; Annotations; Base Sequence; Carbohydrates; Care and treatment; Circular DNA; Comparative analysis; Control; Datasets; Diagnosis; DNA sequencing; Enzymes; Evolution; Fungi; Fungi, Pathogenic; Genes; Genetic analysis; Genome, Mitochondrial; Genomes; Genomics; Humans; Identification and classification; Methods; Mitochondria; Nucleotide sequencing; Pathogenicity; Pathogens; Phylogenetics; Phylogeny; Proteins; Risk factors; Sequence Analysis, DNA; SMRT PacBio sequencing; Software; Soil microorganisms; Species; Sporothrix; Sporothrix - genetics; Sporothrix curviconia; Sporothrix phasma; Sporothrix protearum; Sporothrix variecibatus; Sporotrichosis; Statistical analysis; Transposons; Virulence; Virulence (Microbiology); Netherlands; Sporothrix phasma; SMRT PacBio sequencing; De novo assembly; Comparative genomics; Long-read sequencing; Sporothrix curviconia; Sporothrix protearum; Sporotrichosis; Sporothrix variecibatus
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-022-08736-w

The genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic soil and plant fungi, although pathogenic species capable of causing human infections are also present. The whole-genomes of disease-causing species have already been sequenced and annotated but no comprehensive genomic resources for environmental Sporothrix species are available, thus limiting our understanding of the evolutionary origin of virulence-related genes and pathogenicity. The genome assembly of four environmental Sporothrix species resulted in genome size of ~ 30.9 Mbp in Sporothrix phasma, ~ 35 Mbp in S. curviconia, ~ 38.7 Mbp in S. protearum, and ~ 39 Mbp in S. variecibatus, with a variable gene content, ranging from 8142 (S. phasma) to 9502 (S. variecibatus). The analysis of mobile genetic elements showed significant differences in the content of transposable elements within the sequenced genomes, with the genome of S. phasma lacking several class I and class II transposons, compared to the other Sporothrix genomes investigated. Moreover, the comparative analysis of orthologous genes shared by clinical and environmental Sporothrix genomes revealed the presence of 3622 orthogroups shared by all species, whereas over 4200 genes were species-specific single-copy gene products. Carbohydrate-active enzyme analysis revealed a total of 2608 protein-coding genes containing single and/or multiple CAZy domains, resulting in no statistically significant differences among pathogenic and environmental species. Nevertheless, some families were not found in clinical species. Furthermore, for each sequenced Sporothrix species, the mitochondrial genomes was assembled in a single circular DNA molecule, ranging from 25,765 bp (S. variecibatus) to 58,395 bp (S. phasma). In this study, we present four annotated genome assemblies generated using PacBio SMRT sequencing data from four environmental species: S. curviconia, S. phasma, S. protearum and S. variecibatus with the aim to provide a starting point for future comparative genome evolution studies addressing species diversification, ecological/host adaptation and origin of pathogenic lineages within the genus Sporothrix.