Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Shen, Xing-Xing; Opulente, Dana A.; Kominek, Jacek; Zhou, Xiaofan; Steenwyk, Jacob L.; Buh, Kelly V.; Haase, Max A. B.; Wisecaver, Jennifer H.; Wang, Mingshuang; Doering, Drew T.; Boudouris, James T.; Schneider, Rachel M.; Langdon, Quinn K.; Ohkuma, Moriya; Endoh, Rikiya; Takashima, Masako; Manabe, Ri-ichiroh; Čadež, Neža; Libkind, Diego; Rosa, Carlos A.; DeVirgilio, Jeremy; Hulfachor, Amanda Beth; Groenewald, Marizeth; Kurtzman, Cletus P.; Hittinger, Chris Todd; Rokas, Antonis

doi:10.1016/j.cell.2018.10.023

Title: Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Journal Article · Thu Nov 08 00:00:00 EST 2018 · Cell

DOI:https://doi.org/10.1016/j.cell.2018.10.023· OSTI ID:1506653

Shen, Xing-Xing ^[1]; Opulente, Dana A. ^[2]; Kominek, Jacek ^[2]; Zhou, Xiaofan ^[3]; Steenwyk, Jacob L. ^[1]; Buh, Kelly V. ^[2]; Haase, Max A. B. ^[4]; Wisecaver, Jennifer H. ^[5]; Wang, Mingshuang ^[1]; Doering, Drew T. ^[2]; Boudouris, James T. ^[2]; Schneider, Rachel M. ^[2]; Langdon, Quinn K. ^[2]; Ohkuma, Moriya ^[6]; Endoh, Rikiya ^[6]; Takashima, Masako ^[6]; Manabe, Ri-ichiroh ^[7]; Čadež, Neža ^[8]; Libkind, Diego ^[9]; Rosa, Carlos A. ^[10] more »

Vanderbilt Univ., Nashville, TN (United States)
Univ. of Wisconsin, Madison, WI (United States)
Vanderbilt Univ., Nashville, TN (United States); South China Agricultural University, Guangzhou (China)
Univ. of Wisconsin, Madison, WI (United States); NYU School of Medicine, New York, NY (United States)
Vanderbilt Univ., Nashville, TN (United States); Purdue Univ., West Lafayette, IN (United States)
Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba (Japan)
RIKEN Center for Integrative Medical Sciences, Yokohama (Japan)
University of Ljubljana (Slovenia)
Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue (Argentina)
Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil)
U.S. Department of Agriculture, Peoria, IL (United States)
Westerdijk Fungal Biodiversity Institute, Utrecht (the Netherlands)

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. In this study, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.

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

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Contributing Organization:: Advanced Computing Center for Research and Education at Vanderbilt University; the Center for High-Throughput Computing at the University of Wisconsin—Madison; Lucigen, the CIPRES Science Gateway; and the University of Wisconsin Biotechnology Center DNA Sequencing Facility

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

OSTI ID:: 1506653

Journal Information:: Cell, Vol. 175, Issue 6; ISSN 0092-8674

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 272 works

Citation information provided by
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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
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Additional file 1 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620077 The current record is supplemented by this text	text	January 2021
Additional file 2 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620080 The current record is supplemented by this text	text	January 2021
Additional file 3 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620083.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 4 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620086.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 5 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620089 The current record is supplemented by this dataset	dataset	January 2021
Additional file 6 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620092.v1 The current record is supplemented by this text	text	January 2021
Additional file 7 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620095.v1 The current record is supplemented by this text	text	January 2021
Additional file 8 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620098.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 9 of Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.13620101.v1 The current record is supplemented by this text	text	January 2021
Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii Alva, Troy R.; Riera, Melanie; Chartron, Justin W. https://doi.org/10.6084/m9.figshare.c.5276165 The current record is supplemented by this collection	collection	January 2021