Abstract
Dimorphic organisms possess the remarkable genome capacity to alternate genetic information between two distinct life forms. In dimorphic Mucorales, lineages can reversibly transition between yeast and mycelium as a function of environmental stimuli. However, how genetic information produces two divergent life evolves in a single genome remains unresolved. Here, we report hundreds of gene families exhibiting convergent evolution for dimorphism. This adaptation involves paralog functionalization and the coordination of expression, with yeast and mycelium-specific paralogs. Though these gene families have distinct functions, all their paralogs are convergently adapted to produce yeast and mycelium morphologies. In addition, dimorphic gene families with related functions form head-to-head structures, coordinating differential expression. This coordinated regulation is controlled by two new genes, dkl and dfl. Loss of function of these genes results in global dysregulation of gene expression and loss of dimorphism. Dimorphic gene families, head-to-head marker loci, and the dfl gene are conserved across various dimorphic species but are absent in closely related monomorphic species. Our findings identify an evolutionary mechanism that integrates and optimizes the genetic information required for two distinct life forms within a single organism.
Data availability
The complete raw data that support the findings of this study have been submitted to the Gene Expression Omnibus (GEO) under the accession number GSE293402. Source data are provided with this paper.
Code availability
The complete data analysis pipeline, including all scripts, datasets, annotations, software versions, and auxiliary files required to reproduce the results of this study, is available on GitHub: (https://doi.org/10.5281/zenodo.17662492). Any future updates to the code and supplementary materials will also be provided there.
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Acknowledgements
This research was funded the MCIN/AEI/ 10.13039/501100011033 by “ERDF A way of making Europe,” by the “European Union” (grant PID2021-124674NB-I00 to F.E.N. and V.G.), Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia (20897/PI/18 and 21969/PI/22 to V.G.). We would like to thank Joseph Heitman (Duke University School of Medicine) for his critical review of the original draft.
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G.T. and M.I.N.M. contributed equally to this work. G.T. conducted most of the bioinformatic analyses and reviewed the manuscript draft. M.I.N.M. generated all the HAIUS mutants, contributed to the discovery of the dimorphic gene families, and reviewed the manuscript draft. C.L. conducted bioinformatic analyses and reviewed the manuscript draft. C.P.A. helped with the transcriptomic analyses and reviewed the manuscript draft. G.N.D.S. characterized the phenotype and transcriptome of dkl and dfl mutants. E.N. managed the project and provided materials. V.G. analyzed the results and designed, supervised, and coordinated the project. F.E.N. participated in the generation of mutants, phenotype analyses, bionformatic analyses, wrote the original draft, analyzed the results and designed, supervised, and coordinated the project.
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Tahiri, G., Navarro-Mendoza, M.I., Lax, C. et al. Coordinated gene family evolution shapes the genome of dimorphic Mucorales. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68866-7
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DOI: https://doi.org/10.1038/s41467-026-68866-7
