Moonjely, S. | Search bioRxiv

bioRxiv2025

Comparative transcriptional analysis reveals gene expression changes in spore germination of opportunistic pathogenic fungi

In opportunistic human pathogenic fungi, changes in gene expression play a crucial role in the progression of growth stages from early spore germination through host infection. Comparative transcriptomics between diverse fungal pathogens and non-pathogens provided insights into regulatory mechanisms behind the initiation of infectious processes. We examined the gene expression patterns of 3,845 single-copy orthologous genes (SCOGs) across five phylogenetically distinct species, including the opportunistic human pathogens Fusarium oxysporum, Aspergillus fumigatus, and A. nidulans, and nonpathogenic species Neurospora crassa and Trichoderma asperelloides, at four sequential stages of spore germination. Ancestral status of gene expression was inferred for nodes along the phylogeny. By comparing expression patterns of the SCOGs with their most recent common ancestor (MRCA), we identified genes that exhibit divergent levels of expression during spore germination when comparing fungal pathogens to non-pathogens. We focused on genes related to the MAPK pathway, nitrogen metabolism, asexual development, G-protein signaling, and conidial-wall integrity. Notably, orthologs of the transcription activator abaA, a known central regulator of conidiation, exhibited significant divergence in gene expression in F. oxysporum. This dramatic expression change in abaA was accompanied by structural modifications of phialides in F. oxysporum, and revealed how these changes impact development of offspring, formation of aerial hyphae, spore production, and pathogenicity. Our research provides insights into ecological adaptations observed during the divergence of these species, specifically highlighting how divergence in gene expression during spore germination contributes to their ability to thrive in distinct environments. Author SummaryThe fungi of the phylum Ascomycota include plant and animal pathogens, endophytes, and saprotrophs, some of which are model organisms for biological investigation, and usually have abundant genomic and transcriptomic data. In this study, transcriptomics was studied during spore germination in five species: the opportunistic human pathogens Fusarium oxysporum, Aspergillus fumigatus, and Aspergillus nidulans, and the nonpathogenic species Neurospora crassa and Trichoderma asperelloides. We have inferred divergence in gene expression for 3,845 single-copy orthologous genes (SCOGs) along these lineages. Genes related to the MAPK pathway, nitrogen metabolism, conidia-related regulators, G protein signaling, and conidial-wall integrity exhibited dramatic expression shifts in the lineages of the opportunistic human pathogens evolving towards true pathogenic species. Notably, abaA, a known central regulator of conidiation, exhibited striking divergence in expression in the opportunistic pathogens, resulting in structural modifications in phialides that were more similar to pathogenic species, and revealing how these changes impact development of aerial hyphal formation, spore production, and pathogenicity. These findings provide insights into ecological adaptations resulting from divergence in gene expression, and reveal dynamic transcriptional changes, which may be crucial for the adaptation of opportunistic pathogens to changing environments. By elucidating the shifting roles of abaA, our research contributes to a deeper understanding of the divergence mechanisms underlying development and pathogenicity in fungi.

microbiology↗

bioRxiv2024

Comparative transcriptomics reveal contrasting fungal strategies in a plant pathogen versus an endophyte during initial host colonization

Conidial germination marks the beginning of the fungal life cycle on the host plant, leading to disease or mutually beneficial relationships. Here, we use comparative transcriptomics to unravel the transcriptional similarities and differences during conidial germination and initial colony establishment of the plant pathogen Fusarium graminearum, and the endophyte Metarhizium anisopliae. Our comparison crosses four stages from fresh conidia to polar growth, hyphal extension, ending in either first hyphal branching (on medium) or appressorium formation (on barley). F. graminearum exhibited a higher number of upregulated genes for CAZymes, specialized metabolites and effectors compared to M. anisopliae during the interaction with the host, particularly during the appressorium stage, reflecting its pathogenic nature. The formation of appressoria by M. anisopliae conidia during germination on barley roots has not been documented previously and includes both morphological characteristics and gene expression patterns that regulate appressorium development. Our analysis reveals reduced transcript levels of CAZyme and specialized metabolite genes in M. anisopliae compared to F. graminearum, reflecting a less aggressive host penetration approach. The candidate genes associated with indole-3-acetic acid synthesis were upregulated in M. anisopliae during the appressorium stage, supporting its endophytic lifestyle, and suggesting that the fungus uses a phytohormone based strategy to interact with plant hosts. Collectively, our findings expand the transcriptome resources and provide valuable insights into the gene networks involved in conidial germination and initiation of infection in pathogenic versus endophytic fungi, as well as documenting appressorium formation for the first time, in the endophytic life cycle of M. anisopliae. IMPORTANCEConidial germination is the initial step for fungal colonization in diverse environments. Here we examine the transcriptional similarities and differences in conidial germination and colony establishment of Fusarium graminearum and Metarhizium anisopliae, two fungal species belongs to the Order Hypocreales with distinct lifestyles. F. graminearum is a plant pathogen and the causal agent of Fusarium head blight on cereal crops, whereas M. anisopliae is an insect pathogen and root endophyte which forms beneficial associations with plants. We compared the transcriptome profiles of these species under two nutrient conditions across four stages of conidial germination. Our study shows that the expression profile of the genes encoding carbohydrate-active enzymes, specialized metabolites, and putative effectors varies between F. graminearum and M. anisopliae. The results of this study provide insights into gene networks associated with spore germination stages on the host in a pathogenic versus an endophytic fungus.

microbiology↗