Comparative transcriptional analysis reveals gene expression changes in spore germination of opportunistic pathogenic fungi
Authors: Kim Da-Woon , Ebert Malaika K. , Moonjely Soumya , Wang Zheng , Yarden Oded , Townsend Jeffrey P. , Trail Frances 
Published: February 2025

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 pathogensFusarium oxysporum,Aspergillus fumigatus, andA. nidulans,and nonpathogenic speciesNeurospora crassaandTrichoderma 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 activatorabaA, a known central regulator of conidiation, exhibited significant divergence in gene expression inF. oxysporum. This dramatic expression change inabaAwas accompanied by structural modifications of phialides inF. 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 Summary

The 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 pathogensFusarium oxysporum,Aspergillus fumigatus, andAspergillus nidulans, and the nonpathogenic speciesNeurospora crassaandTrichoderma 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 ofabaA, our research contributes to a deeper understanding of the divergence mechanisms underlying development and pathogenicity in fungi.