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

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

doi:10.1038/s41467-023-36139-2

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

Journal Article · Tue Feb 07 23:00:00 EST 2023 · Nature Communications

DOI:https://doi.org/10.1038/s41467-023-36139-2· OSTI ID:1970475

^[1]; Ubbelohde, Emily J. ^[2]; Kuang, Meihua Christina ^[2]; ^[2]; Langdon, Quinn K. ^[2]; ^[2]; Koshalek, Justin A. ^[2]; Hulfachor, Amanda Beth ^[2]; Opulente, Dana A. ^[2]; Hall, David J. ^[3]; Hyma, Katie ^[4]; Fay, Justin C. ^[4]; Leducq, Jean-Baptiste ^[5]; ^[6]; ^[7]; Libkind, Diego ^[8]; Gonçalves, Carla ^[9]; ^[10]; ^[10]; ^[11] more »

Univ. of Oslo (Norway); Inst. of Agrochemistry and Food Technology (IATA), Valencia (Spain); Univ. of Wisconsin, Madison, WI (United States); University of Wisconsin-Madison Laboratory of Genetics
Univ. of Wisconsin, Madison, WI (United States)
Univ. of Utrecht (The Netherlands)
Univ. of Rochester, NY (United States)
Univ. de Montréal (Canada); Univ. Laval, Quebec City (Canada)
Canada Natural Resources, Quebec City (Canada)
Univ. Laval, Quebec City (Canada)
Científicas y Técnicas (CONICET)-Univ. Nacional del Comahue, Bariloche (Argentina)
Univ. of Wisconsin, Madison, WI (United States); Univ. NOVA de Lisboa, Caparica (Portugal); Vanderbilt Univ., Nashville, TN (United States)
Univ. NOVA de Lisboa, Caparica (Portugal)
Univ. of Wisconsin, Madison, WI (United States); Hebei Univ., Baoding (China)
Chinese Academy of Sciences (CAS), Beijing (China). Inst. of Chemistry

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.

View Accepted Manuscript (DOE)

Research Organization:: Great Lakes Bioenergy Research Center, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Marie Sklodowska-Curie; Research Council of Norway (RCN); Generalitat Valenciana plan GenT; National Science Foundation (NSF); National Natural Science Foundation of China (NSFC)

Grant/Contract Number:: SC0018409; FC02-07ER64494

OSTI ID:: 1970475

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 14; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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