Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

被引：385

作者：

Shen, Xing-Xing ^{[1
]}

Opulente, Dana A. ^{[2
,3
]}

Kominek, Jacek ^{[2
,3
]}

Zhou, Xiaofan ^{[1
,4
]}

Steenwyk, Jacob L. ^{[1
]}

Buh, Kelly V. ^{[2
]}

Haase, Max A. B. ^{[2
,3
,5
]}

Wisecaver, Jennifer H. ^{[1
,6
]}

Wang, Mingshuang ^{[1
]}

Doering, Drew T. ^{[2
]}

Boudouris, James T. ^{[2
]}

Schneider, Rachel M. ^{[2
,3
]}

Langdon, Quinn K. ^{[2
]}

Ohkuma, Moriya ^{[7
]}

Endoh, Rikiya ^{[7
]}

Takashima, Masako ^{[7
]}

Manabe, Ri-ichiroh ^{[8
]}

Cadez, Neza ^{[9
]}

Libkind, Diego ^{[10
]}

Rosa, Carlos A. ^{[11
]}

DeVirgilio, Jeremy ^{[12
]}

Hulfachor, Amanda Beth ^{[2
]}

Groenewald, Marizeth ^{[13
]}

Kurtzman, Cletus P. ^{[12
]}

Hittinger, Chris Todd ^{[2
,3
]}

Rokas, Antonis ^{[1
]}

机构：

[1] Vanderbilt Univ, Dept Biol Sci, 221 Kirkland Hall, Nashville, TN 37235 USA

[2] Univ Wisconsin, JF Crow Inst Study Evolut, Wisconsin Energy Inst, Lab Genet,Genome Ctr Wisconsin, Madison, WI 53706 USA

[3] Univ Wisconsin, DOE Great Lakes Bioenergy Res Ctr, Madison, WI 53706 USA

[4] South China Agr Univ, Integrat Microbiol Res Ctr, Guangdong Prov Key Lab Microbial Signals & Dis Co, Guangzhou 510642, Guangdong, Peoples R China

[5] NYU, Sch Med, Sackler Inst Grad Biomed Sci, New York, NY 10016 USA

[6] Purdue Univ, Dept Biochem, Ctr Plant Biol, W Lafayette, IN 47907 USA

[7] RIKEN, BioResource Res Ctr, Japan Collect Microorganisms, Tsukuba, Ibaraki 3050074, Japan

[8] RIKEN, Ctr Integrat Med Sci, Lab Comprehens Genom Anal, Div Genom Technol,Ctr Life Sci Technol, Yokohama, Kanagawa 2300045, Japan

[9] Univ Ljubljana, Biotech Fac, Ljubljana 1000, Slovenia

[10] Univ Nacl Comahue, Consejo Nacl Invest Cient & Tecn, Inst Andino Patagon Tecnol Biol & Geoambientales, Lab Microbiol Aplicada & Biotecnol,CONICET, RA-8400 San Carlos De Bariloche, Rio Negro, Argentina

[11] Univ Fed Minas Gerais, Dept Microbiol, ICB, CP 486, BR-31270901 Belo Horizonte, MG, Brazil

[12] ARS, Mycotoxin Prevent & Appl Microbiol Res Unit, Natl Ctr Agr Utilizat Res, USDA, Peoria, IL 61604 USA

[13] Westerdijk Fungal Biodivers Inst, NL-3584 CT Utrecht, Netherlands

来源：

CELL | 2018年 / 175卷 / 06期

基金：

美国国家科学基金会;

关键词：

HORIZONTAL GENE-TRANSFER; PHYLOGENETIC ANALYSIS; TREE; TOOL; SEQUENCE; ALGORITHM; FUNGAL; RECONSTRUCTION; ANNOTATION; ALIGNMENTS;

D O I：

10.1016/j.cell.2018.10.023

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale 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 wide-spread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.

引用

页码：1533 / +

页数：33

共 108 条

[71] Molybdenum cofactor biosynthesis and molybdenum enzymes [J].

Schwarz, Guenter ;

Mendel, Ralf R. .

ANNUAL REVIEW OF PLANT BIOLOGY, 2006, 57 :623-647

[72] Contentious relationships in phylogenomic studies can be driven by a handful of genes [J].

Shen, Xing-Xing ;

Hittinger, Chris Todd ;

Rokas, Antonis .

NATURE ECOLOGY & EVOLUTION, 2017, 1 (05)

[73] Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data [J].

Shen, Xing-Xing ;

Zhou, Xiaofan ;

Kominek, Jacek ;

Kurtzman, Cletus P. ;

Hittinger, Chris Todd ;

Rokas, Antonis .

G3-GENES GENOMES GENETICS, 2016, 6 (12) :3927-3939

[74] A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference [J].

Shen, Xing-Xing ;

Salichos, Leonidas ;

Rokas, Antonis .

GENOME BIOLOGY AND EVOLUTION, 2016, 8 (08) :2565-2580

[75] CONSEL: for assessing the confidence of phylogenetic tree selection [J].

Shimodaira, H ;

Hasegawa, M .

BIOINFORMATICS, 2001, 17 (12) :1246-1247

[76] An approximately unbiased test of phylogenetic tree selection [J].

Shimodaira, H .

SYSTEMATIC BIOLOGY, 2002, 51 (03) :492-508

[77] Efficient de novo assembly of large genomes using compressed data structures [J].

Simpson, Jared T. ;

Durbin, Richard .

GENOME RESEARCH, 2012, 22 (03) :549-556

[78] ABySS: A parallel assembler for short read sequence data [J].

Simpson, Jared T. ;

Wong, Kim ;

Jackman, Shaun D. ;

Schein, Jacqueline E. ;

Jones, Steven J. M. ;

Birol, Inanc .

GENOME RESEARCH, 2009, 19 (06) :1117-1123

[79] Horizontal Transfer of a Nitrate Assimilation Gene Cluster and Ecological Transitions in Fungi: A Phylogenetic Study [J].

Slot, Jason C. ;

Hibbett, David S. .

PLOS ONE, 2007, 2 (10)

[80] Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi [J].

Slot, Jason C. ;

Rokas, Antonis .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (22) :10136-10141

← 2 3 4 5 6 7 8 9 10 11 →