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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Emerging Pests and Pathogens Research » Research » Publications at this Location » Publication #427973
Research Project: Management and Biology of Arthropod Pests and Arthropod-borne Plant Pathogens

Location: Emerging Pests and Pathogens Research

Title: Unraveling the genomic and phylogenetic complexity of the understudied microfungus Basidiobolus: Insights from 19 newly sequenced genomes

Author
item CARLETON, JASPER - Clark University
item BRADSHAW, ALEXANDER - Clark University
item CLEARY, LIAM - Clark University
item HINCHER, MADISON - Clark University
item Bushley, Kathryn
item TABIMA, JANVIER - Clark University

Submitted to: Mycologia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/17/2026
Publication Date: 3/13/2026
Citation: Carleton, J.P., Bradshaw, A.J., Cleary, L., Hincher, M.R., Bushley, K.E., Tabima, J.F. 2026. Unraveling the genomic and phylogenetic complexity of the understudied microfungus Basidiobolus: Insights from 19 newly sequenced genomes. Mycologia. 18(3):482-495. https://doi.org/10.1080/00275514.2026.2619989.
DOI: https://doi.org/10.1080/00275514.2026.2619989

Interpretive Summary: Basidiobolus are an ancient and early-diverging genus of fungi known for inhabiting a variety of ecological habitats. Some are pathogens of insects or inhabit vertebrate (frog) gastrointestinal tracts. The taxonomy of these fungi is poorly resolved and in need of revision. Additionally, very little is known about the functional gene content and there is currently only a single genome sequence available for the entire genus. This study sequenced 19 genomes of Basidiobolus from the USDA-Agricultural Research Service Entomopathogenic Fungal collection and conducted phylogenomic analysis to assess systematic relationships and investigate secondary metabolite biosynthetic clusters in these fungi. Results showed two main clades corresponding to two well known species as well as several clades with deep divergence potentially indicative of cryptic species in need of further sampling. Additionally, a variety of secondary metabolite clusters were detected, supporting potential for synthesis of a plethora of natural products. This study provides insights into the biology of these fungi and provides genomic resources that were previously lacking for future studies into these fungi.

Technical Abstract: Basidiobolus is a globally distributed genus of early-diverging fungi within Zoopagomycota, known for its presence in diverse ecological niches ranging from soil and decaying organic matter to vertebrate gastrointestinal tracts. Despite its ecological and medical relevance, the taxonomy and evolutionary relationships within the genus remain poorly resolved due to limited genomic resources. In this study, we present nineteen newly sequenced Basidiobolus genomes, expanding the available genomic data. Using short-read Illumina sequencing, assembly, and annotation pipelines, we characterize gene content, assess completeness, and explore biosynthetic gene content across isolates. Phylogenomic analysis reveals two major clades corresponding to B. meristosporus and B. ranarum, while B. heterosporus forms a distinct lineage. Several isolate clusters exhibit deep divergence suggestive of cryptic species, underscoring the need for expanded sampling and taxonomic revision. Functional annotations reveal a rich repertoire of biosynthetic gene clusters, including non-ribosomal peptide synthetases, polyketide synthases, and hybrid clusters, pointing to an underexplored reservoir of secondary metabolite potential. These findings position Basidiobolus as a compelling model for investigating fungal evolution, ecological adaptation, and natural product biosynthesis.