A Molecular Portrait of De Novo Genes in Yeasts
Abstract
New genes, with novel protein functions, can evolve “from scratch” out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo gene candidates in 15 yeast species from 2 genera whose phylogeny spans at least 100 million years of evolution. We validated 85 candidates by proteomic data, providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from noncoding to coding for 30 Saccharomyces de novo genes. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We also found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. Finally, we found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination contributes to de novo gene emergence in yeasts.
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BibTeX
@article{vakirlis2026molecular,
title = {{A Molecular Portrait of De Novo Genes in Yeasts}},
author = {Nikolaos Vakirlis and Alex Hebert and Dana Opulente and Guillaume Achaz and Chris Todd Hittinger and Gilles Fischer and Joshua J. Coon and Ingrid Lafontaine},
journal = {Molecular Biology and Evolution},
year = {2026},
month = oct,
doi = {10.1093/molbev/msx315},
url = {https://hal.science/hal-02164404v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - A Molecular Portrait of De Novo Genes in Yeasts
AU - Nikolaos Vakirlis
AU - Alex Hebert
AU - Dana Opulente
AU - Guillaume Achaz
AU - Chris Todd Hittinger
AU - Gilles Fischer
AU - Joshua J. Coon
AU - Ingrid Lafontaine
PY - 2026
DA - 2026/10/05
JO - Molecular Biology and Evolution
DO - 10.1093/molbev/msx315
UR - https://hal.science/hal-02164404v1
AB - New genes, with novel protein functions, can evolve “from scratch” out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo gene candidates in 15 yeast species from 2 genera whose phylogeny spans at least 100 million years of evolution. We validated 85 candidates by proteomic data, providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from noncoding to coding for 30 Saccharomyces de novo genes. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We also found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. Finally, we found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination contributes to de novo gene emergence in yeasts.
SN - 0737-4038
SN - 1537-1719
ER -