Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti

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Authors: Nybo, J.L. ¹ ; Vesth, T.C. ¹ ; Theobald, S. ¹ ; Frisvad, J.C. ¹ ; Larsen, T.O. ¹ ; Kjaerboelling, I. ¹ ; Rothschild-Mancinelli, K. ¹ ; Lyhne, E.K. ¹ ; Barry, K. ² ; Clum, A. ² ; Yoshinaga, Y. ² ; Ledsgaard, L. ¹ ; Daum, C. ² ; Lipzen, A. ² ; Kuo, A. ² ; Riley, R. ² ; Mondo, S. ² ; Labutti, K. ² ; Haridas, S. ² ; Pangalinan, J. ² ; Salamov, A.A. ² ; Simmons, B.A. ^{3,
4} ; Magnuson, J.K. ⁴ ; Chen, J. ^{5,
6} ; Drula, E. ^{7,
8} ; Henrissat, B. ¹ ; Wiebenga, A. ⁹ ; Lubbers, R.J.M. ⁹ ; Müller, A. ⁹ ; dos Santos Gomes, A.C. ⁹ ; Mäkelä, M.R. ¹⁰ ; Stajich, J.E. ^{5,
6} ; Grigoriev, I.V. ^{11,
2} ; Mortensen, U.H. ¹ ; de Vries, R.P. ⁹ ; Baker, S.E. ^{12,
4} ; Andersen, M.R. ¹ ;

Source: Studies in Mycology, Volume 111, Number 1, June 2025, pp. 101-114(14)

Publisher: Westerdijk Fungal Biodiversity Institute

DOI: https://doi.org/10.3114/sim.2025.111.03

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers.

Keywords: ASPERGILLUS; CAZYMES; COMPARATIVE GENOMICS; SECONDARY METABOLITES; SECTION CAVERNICOLUS; SECTIONUSTI

Document Type: Research Article

Affiliations: 1: Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark 2: US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 3: Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 4: US Department of Energy Joint Bioenergy Institute, Berkeley, CA, USA 5: Institute for Integrative Genome Biology, University of California, Riverside, CA, USA 6: Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA 7: Biodiversité et Biotechnologie Fongiques, UMR 1163, INRAE, Marseille, France 8: AFMB, UMR 7257 CNRS Aix-Marseille Univ., USC 1408 INRAE, Marseille, France 9: Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands 10: Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland 11: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA 12: Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

Publication date: June 1, 2025

This article was made available online on March 5, 2025 as a Fast Track article with title: "Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti".

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Studies in Mycology is an international journal which publishes systematic monographs of filamentous fungi and yeasts, and special topical issues related to all fields of mycology, biotechnology, ecology, molecular biology, pathology and systematics. The journal is Open-Access and contains monographs or topical issues (5–6 papers per issue). There are no restrictions of length, although it is generally expected that manuscripts should be at least 50 A4 pages in print.
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Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti

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