| The Talaromyces genus was first proposed by Benjamin et al.in 1955 and was originally classified under the Penicillium genus.Later,based on monotypic naming,phylogenetic analyses,and distinctive morphological features,it was renamed Talaromyces in 2011.Members of this fungal genus are widely distributed in both natural and human environments.The impacts of Talaromyces fungi are significant and can be both positive and negative.Some species can degrade cellulose,promote plant growth,act as biocontrol agents against fungal diseases,and have been applied in medicine,food,and cosmetics.However,some species can contaminate food,produce mycotoxins,and even cause infections in humans.Talaromyces species have attracted widespread attention from various research fields such as food,environmental and medical mycology,and biotechnology.Despite the increasing understanding of these various species,their diversity remains poorly understood.The availability of genomic sequences for the Talaromyces genus in public databases is continually increasing,presenting opportunities for studying this fungal genus at the genome level.In this study,we performed pan-genomic and phylogenetic analyses on 70 Talaromyces genomes.Our comparative genomic analysis shows that the Talaromyces pan-genome is vast,with numerous gene families(21,981),but its core genome is relatively small,comprising only 3,254 gene families,which accounts for 14.8%of the pan-genome.The large number of accessory gene families and strain-specific genes generated notable distinctions between the core and pan-genome phylogenetic trees.Using Eggnog-Mappe software,we analyzed the COG functional categories and KEGG pathways of the gene families in the Talaromyces genus and found no meaningful difference in functional enrichment between core and accessory genomes.To investigate the cause of the high diversity of Talaromyces species,we scrutinized gene family gain,loss,expansion,and contraction events across all Talaromyces species.We discovered that gene family gain and expansion events were more common than loss and contraction,and many of these expanded gene families had metabolic functions.We categorized the types of gene duplication events that led to gene family expansion and found that35.3%～55.3% of genes in each Talaromyces species underwent gene duplication,with dispersed duplications being the most common type.Furthermore,we conducted additional analysis of present and absent gene family,which uncovered that specific genes in Talaromyces marneffei contain homologs to the virulence factor Mp1 p,which were acquired through gene gain events in the ancestor of this species.These results indicated that the pathogenicity of Talaromyces marneffei was closely related to its specific genes.As the only thermal-dimorphic fungi within the Talaromyces,Talaromyces marneffei is a highly concerning fungal species,primarily prevalent in Southeast Asia,its hyphae phase transforms into an infectious yeast phase at 37 ℃.Understanding the regulatory mechanisms for this dimorphic transformation was the key factor of its pathogenesis.Talaromyces marneffei infects immunocompromised patients and has a high fatality rate even after drug treatment.Consequently,long-term medication is required to treat and prevent the disease,which may promote the development of fungal resistance.In this study,we explored the distribution of virulence factors,dimorphism gene,and drug resistance genes in each strain of Talaromyces marneffei.We found a large number of virulence factors causing plant disease in all strains.As some species of Talaromyces are capable of causing plant disease,we hypothesize that these genes were inherited from the common ancestor of Talaromyces.Dimorphism genes from other fungi were also found in all Talaromyces marneffei strains.Additionally,virulence factors and dimorphism genes varied across different strains,indicating the complexity of their pathogenesis and dimorphic transformation mechanisms.We detected homologous resistance genes for fluconazole,itraconazole,and micafungin in all strains,suggesting the risk of drug resistance.The survival of intracellular pathogens largely depends on their ability to modulate and influence defense pathways in eukaryotic host cells.To evade a normally functioning immune system,pathogens have developed numerous mechanisms to subvert host immune responses.For instance,Talaromyces marneffei can avoid clearance by the host immune system.Previous research has shown that Mp1 p is a critical virulence factor for the intracellular survival of Talaromyces marneffei,and that it traps the proinflammatory lipid mediator,arachidonic acid(AA),to evade the host innate immune defense.In this study,we aimed to understand the evolutionary origin of Mp1 p in Talaromyces marneffei and elucidate how pathogenic fungi evade host innate immune defenses.Mp1 p is a 462-amino acid protein with two homologous domains,namely lipid binding domain 1(Mp1p-LBD1)and lipid binding domain 2(Mp1p-LBD2).The result of sequence similarity searches with the Mp1p-LBD revealed that homologous proteins could be found in many other pathogenic fungi.By integrating information on taxonomic distribution,phylogenetic relationships,and sequence similarity of the Mp1 p domains,we discovered that the ancestral Mp1p-LBDs were acquired through ancient horizontal gene transfer(HGT)events.Further investigation showed that Mp1 p homologs in Talaromyces marneffei had undergone extensive gene duplications.The Mp1 p gene present in the Talaromyces marneffei genome might have been the result of a gene fusion event that occurred following gene duplication.Combined with the distribution of core genetic phylogenetic tree and Mp1 p homologues in Talaromyces,we found four strains with classification errors.Overall,our findings indicate that the biphasic transformation and pathogenesis of Talaromyces marneffei are complex processes determined by numerous virulence factors,dimorphic transformation,and drug resistance genes,and also reveal the evolutionary mechanism behind the evasion of host innate immune defense by Talaromyces marneffei and underscore the role of gene duplication and HGT in the evolution of how Talaromyces marneffei avoids host immunity.These findings have implications for understanding the evolution,pathogenicity and drug resistance of Talaromyces species and may inform future antifungal therapy.In this study,we conducted pan-genomic model construction,phylogenetic analysis,and gene family evolution analysis to investigate the causes of species diversity in Talaromyces.Our exploration of virulence factors,dimorphic transformation genes,and drug resistance genes in Talaromyces marneffei demonstrated the complexity of its dimorphic transformation and pathogenic mechanisms,and confirmed the risk of drug resistance.Our evolutionary analysis of Mp1 p revealed the crucial role of gene duplication and HGT in the evolution of how Talaromyces marneffei evades host immunity.Overall,our findings provide new insights into the genetic diversity and evolution of virulence factors and drug resistance mechanisms of pathogenic fungi.This provides a theoretical basis for the development of effective antifungal therapy. |
