MAESTRO uncovers tandem paralog dynamics as a core driver of fungal stress adaptation

Hsieh, P.-H.; Sasaki, Y.; Yang, C.-I.; Wu, Z.-Y.; Steindorff, A. S.; Haridas, S.; Ke, J.; Fatma, Z.; Zhao, Z.; Opulente, D. A.; Deng, S.; Hittinger, C. T.; Grigoriev, I. V.; Dien, B.; Zhao, H.; Li, Y.-P.; Yoshikuni, Y.

doi:10.1101/2025.08.29.673034

bioRxiv · 10.1101/2025.08.29.673034

MAESTRO uncovers tandem paralog dynamics as a core driver of fungal stress adaptation

Hsieh, P.-H.·Sasaki, Y.·Yang, C.-I.·Wu, Z.-Y.·Steindorff, A. S.·Haridas, S.·Ke, J.·Fatma, Z.·Zhao, Z.·Opulente, D. A.·Deng, S.·Hittinger, C. T.·Grigoriev, I. V.·Dien, B.·Zhao, H.·Li, Y.-P.·Yoshikuni, Y.

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Abstract

Understanding how fungi adapt to diverse stresses is critical for mitigating emerging drug resistance and harnessing their robustness for biotechnology. Pichia kudriavzevii is a stress-tolerant and intrinsically drug-resistant yeast, with dual industrial and clinical importance. We analyzed 170 strains using MAESTRO, a machine-learning-assisted GWAS pipeline optimized for small cohorts. MAESTRO identified biologically meaningful features and revealed that copy number variation (CNV) of tandem paralogs (TPs) is a core mechanism of multi-stress adaptation. TPs were recurrently linked to tolerance of industrial inhibitors (HMF, phenolics, heat) and antifungal drugs (fluconazole, azoles), and deletion of the TP pair gene4260/gene4261 confirmed pleiotropic effects across stresses. These findings support a TP CNV model where recombination-driven TP CNVs and gene fusions enable rapid stress adaptation. Importantly, our results suggest that antifungal resistance can arise through co-option of mechanisms originally evolved for environmental stressors, raising a One Health concern about the environmental origins of drug-resistant pathogens.

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Hsieh, P.-H., Sasaki, Y., Yang, C.-I., Wu, Z.-Y., Steindorff, A. S., Haridas, S., Ke, J., Fatma, Z., Zhao, Z., Opulente, D. A., Deng, S., Hittinger, C. T., Grigoriev, I. V., Dien, B., Zhao, H., Li, Y.-P., Yoshikuni, Y.. 2025-09-04. MAESTRO uncovers tandem paralog dynamics as a core driver of fungal stress adaptation. https://doi.org/10.1101/2025.08.29.673034

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