Evolutionary origin and population diversity of a cryptic hybrid pathogen

Jacob L. Steenwyk, Sonja Knowles, Rafael W. Bastos, Charu Balamurugan, David Rinker, Matthew E. Mead, Christopher D. Roberts, Huzefa A. Raja, Yuanning Li, Ana Cristina Colabardini, Patrícia Alves Castro, Thaila Fernanda Reis, Adiyantara Gumilang, María Almagro-Molto, Alexandre Alanio, Dea Garcia-Hermoso, Endrews Delbaje, Laís Pontes, Camila Figueiredo Pinzan, Angélica Zaninelli Schreiber, David Canóvas, Rafael Sanchez Luperini, Katrien Lagrou, Egídio Torrado, Fernando Rodrigues, Nicholas H. Oberlies, Xiaofan Zhou, Gustavo H. Goldman () and Antonis Rokas ()
Additional contact information
Jacob L. Steenwyk: Berkeley
Sonja Knowles: University of North Carolina at Greensboro
Rafael W. Bastos: Universidade de São Paulo
Charu Balamurugan: VU Station B #35-1634
David Rinker: VU Station B #35-1634
Matthew E. Mead: VU Station B #35-1634
Christopher D. Roberts: University of North Carolina at Greensboro
Huzefa A. Raja: University of North Carolina at Greensboro
Yuanning Li: 72 Binhai Road
Ana Cristina Colabardini: Universidade de São Paulo
Patrícia Alves Castro: Universidade de São Paulo
Thaila Fernanda Reis: Universidade de São Paulo
Adiyantara Gumilang: VU Station B #35-1634
María Almagro-Molto: Ludwig Maximilian University
Alexandre Alanio: Mycology Department
Dea Garcia-Hermoso: Mycology Department
Endrews Delbaje: Universidade de São Paulo
Laís Pontes: Universidade de São Paulo
Camila Figueiredo Pinzan: Universidade de São Paulo
Angélica Zaninelli Schreiber: State University of Campinas
David Canóvas: Universidad de Sevilla
Rafael Sanchez Luperini: Universidade de São Paulo
Katrien Lagrou: Katholieke Universiteit Leuven
Egídio Torrado: Portugal; ICVS/3B’s-PT Government Associate Laboratory
Fernando Rodrigues: Portugal; ICVS/3B’s-PT Government Associate Laboratory
Nicholas H. Oberlies: University of North Carolina at Greensboro
Xiaofan Zhou: South China Agricultural University
Gustavo H. Goldman: Universidade de São Paulo
Antonis Rokas: VU Station B #35-1634

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract Cryptic fungal pathogens pose disease management challenges due to their morphological resemblance to known pathogens. Here, we investigated the genomes and phenotypes of 53 globally distributed isolates of Aspergillus section Nidulantes fungi and found 30 clinical isolates—including four isolated from COVID-19 patients—were A. latus, a cryptic pathogen that originated via allodiploid hybridization. Notably, all A. latus isolates were misidentified. A. latus hybrids likely originated via a single hybridization event during the Miocene and harbor substantial genetic diversity. Transcriptome profiling of a clinical isolate revealed that both parental subgenomes are actively expressed and respond to environmental stimuli. Characterizing infection-relevant traits—such as drug resistance and growth under oxidative stress—revealed distinct phenotypic profiles among A. latus hybrids compared to parental and closely related species. Moreover, we identified four features that could aid A. latus taxonomic identification. Together, these findings deepen our understanding of the origin of cryptic pathogens.

Date: 2024
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DOI: 10.1038/s41467-024-52639-1

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