Comparative Genomic Data Provide New Insight on the Evolution of Pathogenicity in Sporothrix Species

Abstract

Sporothrix species are commonly isolated from environmental and clinical samples. As common causes of zoonotic mycosis, Sporothrix species may result in localized or disseminated infections, posing considerable threat to animal and human health. However, the pathogenic profiles of different Sporothrix species varied, in virulence, geographic location and host ranges, which have yet to be explored. Analysing the genomes of Sporothrix species are useful for understanding their pathogenicity. In this study, we analyzed the whole genome of 12 Sporothrix species and six S. globosa isolates from different clinical samples in China. By combining comparative analyses with Kyoto Encyclopedia of Genes and Genomes (KEGG), Carbohydrate-Active enZymes (CAZy), antiSMASH, Pfam, and PHI annotations, Sporothrix species showed exuberant primary and secondary metabolism processes. The genome sizes of four main clinical species, i.e., S. brasiliensis, S. schenckii, S. globosa, and S. luriei were significantly smaller than other environmental and clinical Sporothrix species. The contracted genes included mostly CAZymes and peptidases genes that were usually associated with the decay of plants, as well as the genes that were associated with the loss of pathogenicity and the reduced virulence. Our results could, to some extent, explain a habitat shift of Sporothrix species from a saprobic life in plant materials to a pathogenic life in mammals and the increased pathogenicity during the evolution. Gene clusters of melanin and clavaric acid were identified in this study, which improved our understanding on their pathogenicity and possible antitumor effects. Moreover, our analyses revealed no significant genomic variations among different clinical isolates of S. globosa from different regions in China.

Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species

“…DNA sequencing and phylogenetic analyses became more common in the diagnostic scenario from the 2010s onwards [ 10 , 13 , 75 , 108 , 110 , 133 ]. Therefore, most keywords such as ‘fungal DNA’, ‘polymerase chain reaction’, ‘differential diagnosis’, ‘phylogeny’, ‘genotype’, ‘mycological typing techniques’ and ‘molecular diagnostic techniques’, have emerged only during the past decade [ 43 , 49 , 89 , 106 , 107 , 112 , 113 , 115 , 116 , 134 , 135 , 136 , 137 , 138 , 139 , 140 , 141 , 142 , 143 , 144 ]. Judging from the circle size of the keywords, we found that ‘fungal DNA’, ‘molecular diagnostic techniques’, ‘genotype’, ‘polymerase chain reaction’, and ‘molecular sequence data’ were the main research focuses ( Figure 7 , Supplementary Table S2 ).…”

Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens

“…Similarly, the comparison of pathogenic and environmental Sporothrix species revealed that gene loss (i.e. of plant degrading enzymes and virulence inhibitors) is more important than gene gain in the evolution of pathogenesis [ 35 ]. Furthermore, it has been proposed that horizontal gene transfer of virulence genes has shaped the adaptability of Verticillium dahliae subspecies towards different hosts (i.e.…”

Old and New Insights into Sporothrix schenckii Complex Biology and Identification

“…Very recently, comparative studies extended our knowledge on phylogenomics and/or genomic evolution, as well as on pathogenicity/virulence-associated genes, of pathogenic Sporothrix species [ 32 , 33 ]. When showing that Sporothrix species are closely related to Ophiostoma species, one study using a gene family evolutionary analysis revealed that virulence, stress response, protease, cell wall composition, or transporter genes were expanded in Sporothrix species, supporting the genomic evolution of pathogenic Sporothrix species from Ophiostoma species [ 32 ].…”

“…Another study revealed that S. brasiliensis , S. schenckii , S. globosa , and S. luriei had significantly smaller genome sizes than other environmental and clinical Sporothrix species. This contraction mostly involved the genes associated with plant biomass decay such as CAZyme (Carbohydrate Active enZyme) or peptidase encoding genes, as well as the genes associated with loss of pathogenicity and reduced virulence [ 33 ]. This might explain not only an adaptive shift of Sporothrix species from a saprobic life in plant materials to a pathogenic life in mammals but also an increase in their pathogenicity during the evolution [ 33 ].…”

“…This contraction mostly involved the genes associated with plant biomass decay such as CAZyme (Carbohydrate Active enZyme) or peptidase encoding genes, as well as the genes associated with loss of pathogenicity and reduced virulence [ 33 ]. This might explain not only an adaptive shift of Sporothrix species from a saprobic life in plant materials to a pathogenic life in mammals but also an increase in their pathogenicity during the evolution [ 33 ]. Until now, there is no known sexual stage in Sporothrix species [ 34 ], despite the presence of a set of mating or pheromone-response protein-encoding genes in their genomes [ 35 ].…”