Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species
- 1Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France;
- 2Université de Bordeaux, ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, F-33140 Villenave d'Ornon, France;
- 3ENSCBP, Bordeaux INP, 33600 Pessac, France;
- 4Institut Universitaire de France (IUF), 75231 Paris, France
Abstract
Polyploidization events are observed across the tree of life and occur in many fungi, plant, and animal species. During evolution, polyploidy is thought to be an important source of speciation and tumorigenesis. However, the origin of polyploid populations is not always clear, and little is known about the precise nature and structure of their complex genome. Using a long-read sequencing strategy, we sequenced 71 strains from the Brettanomyces bruxellensis yeast species, which is found in anthropized environments (e.g., beer, contaminant of wine, kombucha, and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid genomes, we phased them by using different strategies and found that each subpopulation had a unique polyploidization history with distinct trajectories. The polyploid genomes contain either genetically closely related (with a genetic divergence <1%) or diverged copies (>3%), indicating auto- as well as allopolyploidization events. These latest events have occurred independently with a specific and unique donor in each of the polyploid subpopulations and exclude the known Brettanomyces sister species as possible donors. Finally, loss of heterozygosity events has shaped the structure of these polyploid genomes and underline their dynamics. Overall, our study highlights the multiplicity of the trajectories leading to polyploid genomes within the same species.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275380.121.
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Freely available online through the Genome Research Open Access option.
- Received February 11, 2021.
- Accepted October 25, 2021.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
