Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

OPULENTE, DANA A.; STEENWYK, JACOB L.; WISECAVER, JENNIFER H.; BOUDOURIS, JAMES T.; OHKUMA, MORIYA; MANABE, RI-ICHIROH; ROSA, CARLOS A.; GROENEWALD, MARIZETH; ROKAS, ANTONIS; KOMINEK, JACEK; BUH, KELLY V.; WANG, MINGSHUANG; SCHNEIDER, RACHEL M.; ENDOH, RIKIYA; ?ADE?, NE?A; DEVIRGILIO, JEREMY; KURTZMAN, CLETUS P.; SHEN, XING-XING; ZHOU, XIAOFAN; HAASE, MAX A.B.; DOERING, DREW T.; LANGDON, QUINN K.; TAKASHIMA, MASAKO; LIBKIND, DIEGO; HULFACHOR, AMANDA BETH; HITTINGER, CHRIS TODD

CELL

CELL PRESS

Año: 2018 vol. 175 p. 1533 - 1545

0092-8674

Budding yeasts belonging to the subphylum Saccharomycotina are found in every biome and continent and exhibit levels of genetic diversity comparable to those of plants or animals. The metabolic capabilities of their most famous representatives, such as the baker?s yeast Saccharomyces cerevisiae, have made them the cornerstones of diverse industries. To understand the evolution of the subphylum, we analyzed the genomes of 332 yeast strains, including 221 newly sequenced ones, which represent nearly a third of all known budding yeast species and 79 of 92 genera. We establish a robust genus-level phylogeny comprised of 12 major clades, infer the timescale of yeast diversification from the Devonian to the present, quantify the extent and distribution of horizontal gene transfer (HGT) across budding yeasts, and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the Budding Yeast Common Ancestor (BYCA). These analyses suggest that BYCA was a metabolically complex organism and chronicle a tempo and mode of genomic and phenotypic evolution across an entire subphylum that is characterized by lineage-variable HGT and widespread loss of genes and traits.