Biology subjects

Gibbons, J. G.

Publications and source records attributed to Gibbons, J. G..

9 recordsLinked to original sources

bioRxiv2026

SyntenyPair Explorer: an installation-free, browser-based tool for interactive pairwise genome synteny visualization

Comparisons of genome structure between related organisms are central to understanding genome evolution, gene family dynamics, and the genomic basis of phenotypic variation. Synteny, the conserved co-localization of genes along chromosomes, is most readily interpreted visually, yet many existing synteny visualization tools require local software installation, command-line proficiency, and/or dedicated server infrastructure, and produce static images that cannot be explored interactively. Here, I present SyntenyPair Explorer, a lightweight, installation-free tool for interactive visualization of synteny between two genomes. The application runs entirely within a standard web browser as a single, self-contained HTML file with no external dependencies and no server-side component. SyntenyPair Explorer accepts standard file formats already produced by common comparative genomics workflows, including FASTA genome assemblies (used to compute optional assembly summary statistics), GFF3/GTF gene annotations, and either BLAST tabular output (outfmt 6) or MCScanX collinearity files. Syntenic relationships are resolved by gene-identifier matching between the relationship file and the gene annotations, so that each relationship corresponds to a discrete gene-to-gene link. Interactive features include continuous zoom and pan, gene search with automatic centering of the partner genome on the syntenic counterpart, synteny block coloring, extensively customizable gene highlights and annotation callouts, session saving and restoration, and publication-quality image export. I demonstrate the tool by visualizing structural differences at the alpha-amylase loci between two strains of the industrially important fungus Aspergillus oryzae. SyntenyPair Explorer lowers the technical barrier to interactive synteny visualization and is freely available under the MIT license at https://github.com/GibbonsLabGenomics/SyntenyPair-Explorer, with a live browser-based version at https://gibbonslabgenomics.github.io/SyntenyPair-Explorer/.

bioinformatics↗

bioRxiv2026

Opportunistic pathogenicity in fungi can transcend species boundaries

Multiple fungal lineages have independently evolved the ability to opportunistically infect humans, imposing a major burden on public health. Opportunistic pathogenicity requires the confluence of pre-existing fungal traits that facilitate host colonization (e.g., the ability to grow at 37{degrees}C) and host immune filters that permit the survival of some colonizers (e.g., inborn errors of immunity). Numerous studies have shown that fungal pathogens can exhibit extensive strain-to-strain variation in the ability to cause disease. Moreover, it is also well established that non-pathogenic fungi can occasionally cause severe infections. Together, these observations raise the question: What differentiates opportunistic fungal pathogens from non-pathogens? To address this empirically, we compared phenotypic, metabolomic, and genomic variation between Aspergillus fumigatus, an organism responsible for more than 300,000 infections per year, and Aspergillus fischeri, a close relative that is not considered clinically relevant. By examining 26 phenotypic traits across 16 representative strains of A. fumigatus and 16 of A. fischeri, we found that infection-relevant traits measured under in vitro monoculture conditions showed species-specific distributions, whereas traits measured under in vitro coculture with murine macrophages overlapped. Strikingly, strains of the two species also overlapped in their virulence profiles in an immunocompromised murine model of pulmonary aspergillosis; three strains of A. fischeri exhibited lethality rates of >50% while two A. fumigatus strains were among the least virulent of all 32 strains tested. Consistent with this overlap, we could not associate virulence variation with the presence of specific genomic elements, phenotypic traits, or secondary metabolites. Our results raise the hypothesis that opportunistic pathogenicity can extend beyond the boundaries of individual species. We propose a conceptual model in which the opportunistic pathogenic potential of any fungal strain is the product of complex interactions among numerous genomic, ecological, and host immunity factors.

evolutionary biology↗

bioRxiv2025

Population-Specific Transcriptomic Shifts Underlie Secondary Metabolic Diversification in Aspergillus flavus and the Domestication of Aspergillus oryzae

The genomic signatures of microbial domestication remain poorly understood within the context of natural population variation. Here, we demonstrate that Aspergillus oryzae, the filamentous fungus used in soy sauce production, shares more recent ancestry with a predominantly northern, largely non-aflatoxigenic population of Aspergillus flavus (population C). Strikingly, A. oryzae isolates also overlap with the recently described, clinically enriched A. flavus population D, suggesting the possibility of multiple domestication events. Although A. oryzae exhibits reduced virulence compared to A. flavus, all isolates tested retained pathogenicity in a zebrafish infection model. At the transcriptomic level, Aspergillus populations are significantly differentiated, with distinct responses to population density, indicating that population-specific transcriptomes adapt differently to ecological conditions. These differences extend beyond gene content and are not always explained by phylogenetic relationships, suggesting that phenotypic diversification occurs through the rapid reorganization of transcriptomic architectures. For example, A. oryzae displays significantly elevated expression of a module enriched for carbohydrate metabolism. Population-specific variation is also evident among secondary metabolite (SM) gene clusters. While A. oryzae shows markedly reduced expression of specific SM genes, particularly those involved in aflatoxin biosynthesis, this trend does not extend across the entire secondary metabolome. Using machine- learning-based gene regulatory network inference, we identified population-specific transcriptomic differences linked to distinct transcription factors, with evidence for both cis- and trans-acting regulatory divergence, but no changes in global regulators such as laeA. Together, these findings provide new insights into the domestication of A. oryzae, its global significance, and the microevolution of fungal secondary metabolic pathways. Significance StatementAspergillus flavus poses a significant threat to global agriculture by infecting crops and producing aflatoxin, a potent carcinogen that undermines food safety and international trade. The species is also a major human pathogen causing invasive fungal infections. Here, we demonstrate that A. flavus populations exhibit not only variations in their capacity to produce toxins but also in the way they regulate gene expression in response to environmental cues. These regulatory differences played a key role in the domestication of Aspergillus oryzae, a non-aflatoxigenic relative that has been safely used in food fermentation for centuries. Notably, while A. oryzae exhibits reduced aflatoxin biosynthetic gene expression, it expresses other secondary metabolite genes and retains limited opportunistic pathogenic potential. By revealing how transcriptomic rewiring drives population-level divergence, this work provides new insights into the evolution of toxin production, with broad implications for microbial domestication, crop protection, and global food security.

microbiology↗

bioRxiv2025

Divergent Volatile Metabolomes and Flavor Attributes in Rice Fermented by Aspergillus oryzae and Aspergillus flavus

The generally recognized as safe (GRAS) fungus Aspergillus oryzae has been used for millennia in the production of traditional Asian fermented foods and beverages. This prolonged domestication has led to phenotypic adaptations that distinguish A. oryzae from its wild relative, Aspergillus flavus. While genomic and phenotypic differences between these species have been partially characterized, their comparative production of volatile compounds during food fermentation remains poorly understood. Here, we evaluated alpha-amylase activity, aflatoxin production, taste attributes (via electronic tongue), and volatile profiles (via dynamic headspace gas chromatography-mass spectrometry) of the food-grade strain A. oryzae RIB40 and two wild A. flavus strains, NPK13tox and AflaGuard. A. oryzae RIB40 exhibited significantly higher alpha-amylase activity during rice fermentation, and only A. flavus NPK13tox produced aflatoxin. Sensory analysis revealed that rice fermented by A. oryzae RIB40 exhibited more favorable taste attributes, including significantly lower astringency, aftertaste, and bitterness, as well as significantly higher richness (defined as umami aftertaste). Additionally, A. oryzae RIB40 produced a greater number and higher concentrations of volatile compounds, with 20 compounds significantly elevated compared to rice fermented by A. flavus. Many of these volatiles, including 2-methyl-3-buten-2-ol, 3-octen-2-one, 2-methyl-butanal, and 3-methyl-butanal, are associated with pleasant sensory attributes and have previously been linked to A. oryzae-fermented foods. These findings suggest that the volatilome of A. oryzae RIB40 has been shaped by domestication to produce a more desirable sensory profile, enriched in alcohols, aldehydes, ketones, and heterocyclic compounds contributing fruity, umami, and malty notes.

evolutionary biology↗

bioRxiv2023

Chemical mutagenesis of Listeria monocytogenes for increased tolerance to benzalkonium chloride shows independent genetic underpinnings and off-target antibiotic resistance

Listeria monocytogenes, a potentially fatal foodborne pathogen commonly found in food processing facilities, creates a significant economic burden that totals more than $2 billion annually in the United States due to outbreaks. Quaternary ammonium compounds (QACs), including benzalkonium chloride (BAC), are among the most widely used sanitizers to inhibit the growth and spread of L. monocytogenes from food processing facilities. However, resistance to QACs has been increasing in L. monocytogenes and different genetic mechanisms conferring resistance have been discovered. Here, we used ethyl methanesulfonate (EMS) to chemically mutagenize the BAC-susceptible strain, L. monocytogenes FSL-N1-304. We isolated two mutants with increased tolerance to BAC compared to the parental strain. Next, we assessed the off-target effect of increased tolerance to BAC by measuring the minimum inhibitory concentrations (MICs) of a diverse set of antibiotics, revealing that mut-1 and mut-2 displayed significantly increased resistance to fluoroquinolone antibiotics compared to the parental strain. We then sequenced the genomes of the parental strain and both mutants to identify mutations that may be involved in the increased resistance to BAC. We identified 3 and 29 mutations in mut-1 and mut-2, respectively. mut-1 contained nonsynonymous mutations in dagK (a diacylglycerol kinase), lmo2768 (a permease-encoding gene), and lmo0186 (resuscitation promoting factor). mut-2 contained a nonsense mutation in the nucleotide excision repair enzyme UvrABC system protein B encoding gene, uvrB, which likely accounts for the higher number of mutations observed. Transcriptome analysis in the presence of BAC revealed that genes related to the phosphotransferase system and internalins were upregulated in both mutants, suggesting their significance in the BAC stress response. These two mutants provide insights into alternative mechanisms for increased BAC tolerance and could further our understanding of how L. monocytogenes persists in the food processing environment.

microbiology↗

bioRxiv2023

Population genomics of Aspergillus sojae is shaped by the food environment

Traditional fermented foods often contain specialized microorganisms adapted to the unique food environment. For example, the filamentous mold Aspergillus oryzae, used in sake fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor, Aspergillus flavus. Similarly, Aspergillus sojae is used in soybean-based food fermentations (e.g. miso and shochu) and is closely related to Aspergillus parasiticus. Here, we investigated the impact of long-term A. sojae usage in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 12 A. sojae and 10 A. parasiticus genomes, along with phenotypic characteristics of 15 isolates. Our results revealed that A. sojae isolates formed a distinct population separate from A. parasiticus and displayed remarkably low levels of genetic diversity, indicative of a recent clonal expansion. Genome comparisons revealed numerous loss-of-function mutations in A. sojae, notably in genes responsible for secondary metabolite production, including genes in the aflatoxin encoding gene cluster. Consequently, A. sojae lacked aflatoxin production, while it varied among A. parasiticus isolates. No other significant differences were observed in growth rates or other measured phenotypic traits between A. sojae and A. parasiticus. These findings suggest that A. sojae may have evolved from a population of A. parasiticus and lost the ability to produce some secondary metabolites. To elucidate the phenotypic differences between A. sojae and A. parasiticus, future work should focus on the influence of wild and food-associated strains on the sensory aspects and microbial community dynamics of fermented soy products. Significance StatementLike plants and animals, microbes were also domesticated by humans, however relatively little is known about how the process of domestication shapes microbial genomes and traits. We found that isolates of Aspergillus sojae, a mold used in the production of miso and soy sauce, makeup a less toxic group that is genetically distinct from its closely related wild ancestor Aspergillus parasiticus. Our analyses shed new light on commonalities observed across filamentous molds adapted to the food environment.

evolutionary biology↗

bioRxiv2022

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. However, the use of one or few molecular markers can lead to inaccurate inferences of species history and errors in classification. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense dataset of 711 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provide profile Hidden Markov Models for each, facilitating others to use these molecular markers. Examination of the resulting genome-scale phylogeny: (1) helped resolve ongoing taxonomic controversies and identified new ones; (2) revealed extensive strain misidentification, underscoring the importance of population-level sampling in species classification; and (3) identified novel lineages that may shed light on the early evolution of an important genus. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the tree of life.

evolutionary biology↗

bioRxiv2022

Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus

Aspergillus fumigatus is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across A. fumigatus isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 A. fumigatus isolates (133 clinical and 73 environmental isolates) aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanCore genome of A. fumigatus constitutes 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (CORE) and 5,312 (40.6%) vary in their gene presence across isolates (ACCESSORY). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical vs. environmental isolates when accounting for phylogeny. Orthologs that differ in their distribution across isolates tend to occur in low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of A. fumigatus is high. These results suggest that differences in the distribution of orthologs within A. fumigatus cannot be associated with the clinical or environmental origin of isolates. ImportanceAspergillus fumigatus is a cosmopolitan species of fungi responsible for thousands of cases of invasive disease. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, including differences related to virulence and antifungal drug resistance. A comprehensive survey of the genomic diversity present in A. fumigatus and its relationship to the clinical or environmental origin of isolates can contribute to the prediction of the mechanisms of evolution and infection of the species. Our results suggest that there is no significant variation in ortholog distribution between clinical and environmental isolates when accounting for evolutionary history. The work supports the hypothesis that environmental and clinical isolates of A. fumigatus do not differ in their gene contents.

bioinformatics↗

bioRxiv2020

Genome-Wide Association for Itraconazole Sensitivity in Non-Resistant Clinical Isolates of Aspergillus fumigatus

Aspergillus fumigatus is a potentially lethal opportunistic pathogen that infects over [~]200,000 people and causes [~]100,000 deaths per year globally. Treating A. fumigatus infections is particularly challenging because of the recent emergence of azole-resistance. The majority of studies focusing on the molecular mechanisms underlying azole resistance have examined azole-resistant isolates. However, isolates that are susceptible to azoles also display variation in their sensitivity, presenting a unique opportunity to identify genes contributing to azole sensitivity. Here, we used genome-wide association (GWA) analysis to identify loci involved in azole sensitivity by analyzing the association between 68,853 SNPs and itraconazole (ITCZ) minimum inhibitory concentration (MIC) in 76 clinical isolates of A. fumigatus from Japan. Population structure analysis suggests the presence of four distinct populations, with ITCZ MICs distributed relatively evenly across populations. We independently conducted GWA when treating ITCZ MIC as a quantitative trait and a binary trait and identified two SNPs with strong associations that were identified in both analyses. These SNPs fell within the coding regions of Afu2g02220 and Afu2g02140. We functionally validated Afu2g02220 by knocking it out using a CRISPR/Cas-9 approach, because orthologs of this gene are involved in sterol modification and ITCZ targets the ergosterol pathway. Knockout strains displayed no difference in growth compared to the parent strain in minimal media, yet a minor but consistent inhibition of growth in the presence of 0.15 ug/ml ITCZ. Our results suggest that GWA paired with efficient gene deletion is a powerful and unbiased strategy for identifying the genetic basis of complex traits in A. fumigatus. ImportanceAspergillus fumigatus is a pathogenic mold that can infect and kill individuals with compromised immune systems. The azole class of drugs provide antifungal activity against A. fumigatus infections and have become an essential treatment strategy. Unfortunately, A. fumigatus azole resistance has recently emerged and rapidly risen in frequency making treatment more challenging. Our understanding of the molecular basis of azole sensitivity has been shaped mainly through candidate gene studies. Unbiased approaches are necessary to understand the full repertoire of genes and genetic variants underlying azole resistance and sensitivity. Here, we provide the first application of genome-wide association analysis in A. fumigatus in the identification of a gene (Afu2g02220) that contributes to itraconazole susceptibility. Our approach, which combines association mapping and CRISPR/Cas-9 for functional validation of candidate genes, has broad application for investigating the genetic basis of complex traits in fungal systems.

genomics↗