Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species

Goncalves, C.; Steenwyk, J. L.; Rinker, D.; Opulente, D. A.; LaBella, A. L.; Harrison, M.-C.; Wolters, J. F.; Zhou, X.; Shen, X.-X.; Covo, S.; Groenewald, M.; Hittinger, C. T.; Rokas, A.

doi:10.1101/2025.03.15.643480

bioRxiv · 10.1101/2025.03.15.643480

Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species

Goncalves, C.·Steenwyk, J. L.·Rinker, D.·Opulente, D. A.·LaBella, A. L.·Harrison, M.-C.·Wolters, J. F.·Zhou, X.·Shen, X.-X.·Covo, S.·Groenewald, M.·Hittinger, C. T.·Rokas, A.

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Abstract

Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing DNA repair genes. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina to examine the relationship between reduced DNA repair repertoires and elevated evolutionary rates. We identified three distantly related lineages--encompassing 12% of species--with substantially reduced sets of DNA repair genes and the highest evolutionary rates in the entire subphylum. Two of these "faster-evolving lineages" (FELs)--a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)--are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of DNA repair gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. Genomic signatures in the W/S clade are consistent with a substantial mutational burden, including pronounced A|T bias and signatures of endogenous DNA damage. The W/S clade appears to mitigate UV-induced damage through horizontal acquisition of a bacterial photolyase gene, underscoring how gene loss may be offset by nonvertical evolution. These findings highlight how the loss of DNA repair genes gave rise to hypermutators that persist across macroevolutionary timescales, with horizontal gene transfer as an avenue for partial functional compensation.

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Goncalves, C., Steenwyk, J. L., Rinker, D., Opulente, D. A., LaBella, A. L., Harrison, M.-C., Wolters, J. F., Zhou, X., Shen, X.-X., Covo, S., Groenewald, M., Hittinger, C. T., Rokas, A.. 2025-03-17. Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species. https://doi.org/10.1101/2025.03.15.643480

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