Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

David Peris (), Emily J. Ubbelohde, Meihua Christina Kuang, Jacek Kominek, Quinn K. Langdon, Marie Adams, Justin A. Koshalek, Amanda Beth Hulfachor, Dana A. Opulente, David J. Hall, Katie Hyma, Justin C. Fay, Jean-Baptiste Leducq, Guillaume Charron, Christian R. Landry, Diego Libkind, Carla Gonçalves, Paula Gonçalves, José Paulo Sampaio, Qi-Ming Wang, Feng-Yan Bai, Russel L. Wrobel and Chris Todd Hittinger ()
Additional contact information
David Peris: University of Wisconsin-Madison
Emily J. Ubbelohde: University of Wisconsin-Madison
Meihua Christina Kuang: University of Wisconsin-Madison
Jacek Kominek: University of Wisconsin-Madison
Quinn K. Langdon: University of Wisconsin-Madison
Marie Adams: Biotechnology Center, University of Wisconsin-Madison
Justin A. Koshalek: Biotechnology Center, University of Wisconsin-Madison
Amanda Beth Hulfachor: University of Wisconsin-Madison
Dana A. Opulente: University of Wisconsin-Madison
David J. Hall: University of Utrecht
Katie Hyma: University of Rochester
Justin C. Fay: University of Rochester
Jean-Baptiste Leducq: Université de Montréal
Guillaume Charron: Laurentian Forestry Centre
Christian R. Landry: Université Laval
Diego Libkind: Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue
Carla Gonçalves: University of Wisconsin-Madison
Paula Gonçalves: Universidade Nova de Lisboa
José Paulo Sampaio: Universidade Nova de Lisboa
Qi-Ming Wang: University of Wisconsin-Madison
Feng-Yan Bai: Chinese Academy of Sciences
Russel L. Wrobel: University of Wisconsin-Madison
Chris Todd Hittinger: University of Wisconsin-Madison

Nature Communications, 2023, vol. 14, issue 1, 1-19

Abstract: Abstract Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

Date: 2023
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DOI: 10.1038/s41467-023-36139-2

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