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

• Published in: Nature communications Vol. 14; no. 1; pp. 690 - 19
• Main Authors: Peris, David, Ubbelohde, Emily J., Kuang, Meihua Christina, Kominek, Jacek, Langdon, Quinn K., Adams, Marie, Koshalek, Justin A., Hulfachor, Amanda Beth, Opulente, Dana A., Hall, David J., Hyma, Katie, Fay, Justin C., Leducq, Jean-Baptiste, Charron, Guillaume, Landry, Christian R., Libkind, Diego, Gonçalves, Carla, Gonçalves, Paula, Sampaio, José Paulo, Wang, Qi-Ming, Bai, Feng-Yan, Wrobel, Russel L., Hittinger, Chris Todd
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08-02-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/23; 631/136/334/2243/1796; 631/181/2474; 631/181/457; 631/181/757; 631/61/252/171/1495; 64; BASIC BIOLOGICAL SCIENCES; Biodiversity; Eukaryotes; Evolutionary genetics; Food microbiology; Galactose; Gene flow; Gene sequencing; Genetic diversity; Genomes; Geographical distribution; Humanities and Social Sciences; Microorganisms; multidisciplinary; Phenotype; Phylogenetics; Phylogeny; Population genetics; Population structure; Saccharomyces; Saccharomyces - genetics; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Science; Science (multidisciplinary); Species diversity; Substrates; Yeast; Yeasts
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-36139-2

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.
Here, the authors describe the geographies, hosts, substrates, and phylogenetic relationships for 1,794
Saccharomyces
strains. They provide insight into the genetic and phenotypic diversity in the genus, not seen through prior work focused on the model species
Saccharomyces cerevisiae
.