Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Abstract

Background The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. Results Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. Conclusions The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.

Cerebrovascular Complications Associated With Iatrogenic Fungal Meningitis Following Surgical Procedures in Mexico

“…They are highly resistant to typical antifungals and cause a broad spectrum of infections. 7 In October 2022, a meningitis outbreak, which killed 34 patients, following cesarean sections in Mexico attributed to contaminated bupivacaine with F. solani was documented. 8 Although CVC secondary to this fungus have not been reported, 3 cases of ischemic stroke and 1 of cerebral vasculitis and hemorrhagic stroke caused by Exserohilum rostratum have been described 3,9 In 2012, 66 patients affected by a fungal outbreak secondary to epidural anesthesia were investigated; of these, 13 were complicated by ischemic stroke.…”

Pathogenicity, Host Resistance, and Genetic Diversity of Fusarium Species under Controlled Conditions from Soybean in Canada

“…Clade2 included all the isolates identified as F. acuminatum and its reference sequence, with a bootstrap value of 89%. Clade3 included one F. solani, one F. falciforme, and the F. solani reference sequence in the FSSC, with a bootstrap value of 99% [81]. NSRR22_230_white4_SK_F.…”

OMICS and Other Advanced Technologies in Mycological Applications

“…Moreover, phylogenomic studies have greatly improved our understanding of the tree of life and offered directions for future fungal phylogenetic and taxonomic studies [ 110 ]. Large datasets of fungal genomic and transcriptomic data have enabled the study of fungal evolution from a molecular sequence perspective in various fungal groups, i.e., the Fusarium solani species complex [ 111 , 112 ], microsporidia [ 113 ], asexual/sexual aspergilli [ 114 ], Coprinopsis cinerea and Pleurotus pulmonarius [ 115 , 115 ], arbuscular mycorrhizal Paraglomus occultum [ 116 ], and Coccidioides immiti [ 117 ]. WGS of diverse fungal taxa has revealed valuable information regarding large-scale genetic changes, including variations in chromosome structure and number that occurred during the evolution of fungi [ 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 ].…”