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.