Fermentation innovation through complex hybridization of wild and domesticated yeasts

Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast

(2019) Xueying C. Li et al.   Science Advances

Mitochondrial DNA and temperature tolerance in lager yeasts

(2019) EmilyClare P. Baker et al.   Science Advances

Laboratory Evolution of a Saccharomyces cerevisiae × S. eubayanus Hybrid Under Simulated Lager-Brewing Conditions

(2019) Arthur R. Gorter de Vries et al.   Frontiers in Genetics

Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function

(2019) EmilyClare P. Baker et al.   PLoS Genetics

Factors driving metabolic diversity in the budding yeast subphylum

(2018) Dana A. Opulente et al.   BMC BIOLOGY

Origins, evolution, domestication and diversity of Saccharomyces beer yeasts

(2018) Brigida Gallone et al.   CURRENT OPINION IN BIOTECHNOLOGY

Diverse yeasts for diverse fermented beverages and foods

(2018) Chris Todd Hittinger et al.   CURRENT OPINION IN BIOTECHNOLOGY

Multiple rounds of artificial selection promote microbe secondary domestication – the case of cachaça yeasts

(2018) Raquel Barbosa et al.   Genome Biology and Evolution

A comparison of the performance of natural hybrids Saccharomyces cerevisiae  ×  Saccharomyces kudriavzevii at low temperatures reveals the crucial role of their S. kudriavzevii genomic contribution

(2018) Guadalupe Ortiz-Tovar et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication

(2018) Jean-Luc Legras et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The origin and adaptive evolution of domesticated populations of yeast from Far East Asia

(2018) Shou-Fu Duan et al.   Nature Communications

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction

(2018) Kristoffer Krogerus et al.   Frontiers in Microbiology

Selection of Pof-Saccharomyces eubayanus Variants for the Construction of S. cerevisiae × S. eubayanus Hybrids With Reduced 4-Vinyl Guaiacol Formation

(2018) Jasper A. Diderich et al.   Frontiers in Microbiology

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites

(2017) Pedro Almeida et al.   MOLECULAR ECOLOGY

Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species

(2017) David Peris et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

On the origins and industrial applications of Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrids

(2017) David Peris et al.   YEAST

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts

(2016) Margarida Gonçalves et al.   CURRENT BIOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

(2016) X. Zhou et al.   G3-Genes Genomes Genetics

Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae

(2016) Anthony R. Borneman et al.   G3-Genes Genomes Genetics

Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus

(2016) David Peris et al.   PLoS Genetics

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

(2015) M. van den Broek et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Negative epistasis: a route to intraspecific reproductive isolation in yeast?

(2015) Jing Hou et al.   CURRENT GENETICS

Saccharomyces eubayanusandSaccharomyces arboricolareside in North Island native New Zealand forests

(2015) Velimir Gayevskiy et al.   ENVIRONMENTAL MICROBIOLOGY

S. cerevisiae × S. eubayanus interspecific hybrid, the best of both worlds and beyond

(2015) Marit Hebly et al.   FEMS YEAST RESEARCH

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

The Genome Sequence ofSaccharomyces eubayanusand the Domestication of Lager-Brewing Yeasts

(2015) EmilyClare Baker et al.   MOLECULAR BIOLOGY AND EVOLUTION

A population genomics insight into the Mediterranean origins of wine yeast domestication

(2015) Pedro Almeida et al.   MOLECULAR ECOLOGY

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

Dosage compensation can buffer copy-number variation in wild yeast

(2015) James Hose et al.   eLife

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations

(2014) Jordi Tronchoni et al.   BMC GENOMICS

Evidence for a Far East Asian origin of lager beer yeast

(2014) Jian Bing et al.   CURRENT BIOLOGY

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

(2014) Anders Bergström et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing and Characterisation of Rearrangements in Three S. pastorianus Strains Reveals the Presence of Chimeric Genes and Gives Evidence of Breakpoint Reuse

(2014) Sarah K. Hewitt et al.   PLoS One

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum

(2014) Pedro Almeida et al.   Nature Communications

Genome Sequence of Saccharomyces carlsbergensis , the World’s First Pure Culture Lager Yeast

(2014) Andrea Walther et al.   G3-Genes Genomes Genetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome

(2013) Gianni Liti et al.   BMC GENOMICS

Regulations of sugar transporters: insights from yeast

(2013) J. Horák   CURRENT GENETICS

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

(2013) D. A. Skelly et al.   GENOME RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Saccharomyces diversity and evolution: a budding model genus

(2013) Chris Todd Hittinger   TRENDS IN GENETICS

Comparative physiology and fermentation performance of Saaz and Frohberg lager yeast strains and the parental speciesSaccharomyces eubayanus

(2013) Brian R. Gibson et al.   YEAST

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329

(2012) Dao-Qiong Zheng et al.   BMC GENOMICS

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments

(2012) B. Dunn et al.   GENOME RESEARCH

Whole-Genome Sequencing of Sake Yeast Saccharomyces cerevisiae Kyokai no. 7

(2011) T. Akao et al.   DNA RESEARCH

Quantifying the individual effects of ethanol and temperature on the fitness advantage of Saccharomyces cerevisiae

(2011) Z. Salvadó et al.   FOOD MICROBIOLOGY

Evidence for Divergent Evolution of Growth Temperature Preference in Sympatric Saccharomyces Species

(2011) Paula Gonçalves et al.   PLoS One

Deciphering the Hybridisation History Leading to the Lager Lineage Based on the Mosaic Genomes of Saccharomyces bayanus Strains NBRC1948 and CBS380T

(2011) Huu-Vang Nguyen et al.   PLoS One

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

(2011) D. Libkind et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

(2011) Devin R. Scannell et al.   G3-Genes Genomes Genetics

Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae

(2011) Anthony R. Borneman et al.   PLoS Genetics

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Remarkably ancient balanced polymorphisms in a multi-locus gene network

(2010) Chris Todd Hittinger et al.   NATURE

Multiple Molecular Mechanisms Cause Reproductive Isolation between Three Yeast Species

(2010) Jui-Yu Chou et al.   PLOS BIOLOGY

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae

(2009) Nobuhiko Mukai et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

(2009) Leonid Teytelman et al.   PLoS One

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

(2009) M. Novo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Populations of Saccharomyces kudriavzevii in Portugal Are Associated with Oak Bark and Are Sympatric with S. cerevisiae and S. paradoxus

(2008) J. P. Sampaio et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Incompatibility of Nuclear and Mitochondrial Genomes Causes Hybrid Sterility between Two Yeast Species

(2008) Hsin-Yi Lee et al.   CELL

Comparative genome analysis of aSaccharomyces cerevisiaewine strain

(2008) Anthony R. Borneman et al.   FEMS YEAST RESEARCH

Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

(2008) B. Dunn et al.   GENOME RESEARCH