Biology subjects

Trail, F.

Publications and source records attributed to Trail, F..

5 recordsLinked to original sources

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↗

bioRxiv2022

Orphan genes are clustered with allorecognition loci and may be involved in incompatibility and speciation in Neurospora

Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. However, there is a lack of working hypotheses as to how they might play that role. In the genome of Neurospora crassa, most of the 670 Neurospora LSGs that are aggregated adjacent to the telomeres are clustered with 61% of the HET-domain genes, which regulate self-recognition and define vegetative incompatibility groups. Among the 342 LSGs that are dynamically expressed during both asexual and sexual phases, 64% were detectable on unusual carbon sources such as furfural and HMF--wildfire-produced chemicals that are a strong inducer of sexual development. Expression of a significant portion of the LSGs was sensitive to light and temperature, factors that regulate the switch from asexual to sexual reproduction. Furthermore, expression of the LSGs was significantly affected in the knockouts of adv-1 and pp-1 that regulate hyphal communication, and expression of more than one quarter of the LSGs was affected by perturbation of the mating locus. Accordingly, we propose a gene-by-environment interaction model encouraging further investigation of the roles of LSGs and HET-domain genes in speciation in Neurospora. This gene-by-environment interaction model emphasizes the roles of the LSGs in response to genetic and environmental factors, leading to the regulation of the switch from the asexual growth and fusion, such that vegetative incompatibility governed by allorecognition promotes allelic homogeneity, sexual reproduction, and outbreeding, whereas VI repression and meiotic recombination promotes allelic polymorphism.

evolutionary biology↗

bioRxiv2021

Non-target impacts of fungicide disturbance on phyllosphere yeasts in different crop species and management systems

O_LIFungicides reduce fungal pathogen populations and are essential to food security. Fungicide disturbance of plant microbiomes has received limited attention. Understanding the impacts of fungicides on crop microbiomes in different cropping systems is vital to minimizing unintended consequences while maintaining their use for plant protection. C_LIO_LIWe used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage managements. We examine fungicide disturbance and microbiome resilience across these treatments. C_LIO_LIFoliar fungicides directly affected phyllosphere fungal communities, but not root fungal communities or prokaryote communities. Impacts on fungal phyllosphere composition and resiliency were management-dependent and lasted more than thirty days. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially the Bulleribacidiaceae, including core microbiome members. C_LIO_LIFungicide application reduced network complexity in the soybean phyllosphere. Bulleribacidiaceae often co-occurred with Sphingomonas and Hymenobacter in control plots, but co-occurrences were altered in fungicide plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. No-till management was more resilient following fungicide disturbance and recovery. C_LI

microbiology↗

bioRxiv2018

Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum

Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecia, the sexual fruiting bodies of Fusarium graminearum. We have identified 547 lncRNAs whose expression was developmental stage-specific, with about 40% of which peaked during the development of asci, the sac-like structures containing meiospores. A large fraction of the lncRNAs were found to be antisense to mRNAs, forming 300 sense-antisense pairs. Although small RNAs (sRNAs) were produced from these overlapping loci, most of the antisense lncRNAs appeared not to be involved in gene silencing pathways. Genome-wide analysis of sRNA clusters identified many silenced loci at the meiotic stage. However, we found transcriptionally-active sRNA clusters, many of which were associated with lncRNAs. Also, we observed that many antisense lncRNAs and their respective sense transcripts were induced in parallel as the perithecia matured. To identify regulatory components for lncRNA expression, we analyzed mutants defective in the nonsense-mediated decay (NMD) pathway. A subset of the lncRNAs appeared to be targeted by the NMD before the perithecia formation, suggesting a suppressive role of the NMD in lncRNA expression during vegetative stage. This research provides fundamental genomic resources that will spur further investigations on developmental lncRNAs that may play important roles in shaping the fungal fruiting bodies.

developmental biology↗