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

Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast Saccharomyces cerevisiae and a set of closely related species have been instrumental in showing the benefit of analyzing patterns of sequence conservation. Increasing the number of closely related genome sequences makes the comparative genomics approach more powerful and accurate. Here, we report the genome sequence and analysis of Saccharomyces arboricolus, a yeast species recently isolated in China, that is closely related to S. cerevisiae. We obtained high quality de novo sequence and assemblies using a combination of next generation sequencing technologies, established the phylogenetic position of this species and considered its phenotypic profile under multiple environmental conditions in the light of its gene content and phylogeny. We suggest that the genome of S. arboricolus will be useful in future comparative genomics analysis of the Saccharomyces sensu stricto yeasts.

• Publication year

  2013

• Venue

  BMC Genomics

• Publication date

  2013-01-31

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/1471-2164-14-69PMID 23368932PMCID 3599269
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Conservation of replication timing reveals global and local regulation of replication origin activity

  2012cited by this paper
• The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

  2011influential reference
• Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

  2011cited by this paper
• Saccharomyces Genome Database: the genomics resource of budding yeast

  2011cited by this paper
• From sequence to function: Insights from natural variation in budding yeasts☆

  2011cited by this paper
• Removing Noise From Pyrosequenced Amplicons

  2011cited by this paper
• OriDB, the DNA replication origin database updated and extended

  2011cited by this paper
• Trait Variation in Yeast Is Defined by Population History

  2011influential reference
• Co-Evolution of Transcriptional Silencing Proteins and the DNA Elements Specifying Their Assembly

  2010cited by this paper
• Yeast evolutionary genomics

  2010cited by this paper
• Remarkably ancient balanced polymorphisms in a multi-locus gene network

  2010cited by this paper
• Genetic identification of new biological species Saccharomyces arboricolus Wang et Bai

  2010cited by this paper
• Using the Generic Synteny Browser (GBrowse_syn)

  2010cited by this paper
• Accurate determination of microbial diversity from 454 pyrosequencing data

  2009cited by this paper
• Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production.

  2009cited by this paper
• Recent advances in the biological production of mannitol

  2009cited by this paper
• Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

  2009cited by this paper
• Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

  2009cited by this paper
• BFAST: An Alignment Tool for Large Scale Genome Resequencing

  2009cited by this paper
• Natural Populations of Saccharomyces kudriavzevii in Portugal Are Associated with Oak Bark and Are Sympatric with S. cerevisiae and S. paradoxus

  2008cited by this paper
• Population genomics of domestic and wild yeasts

  2008cited by this paper
• Saccharomyces arboricolus sp. nov., a yeast species from tree bark.

  2008influential reference
• Chemogenetic fingerprinting by analysis of cellular growth dynamics

  2008cited by this paper
• Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.

  2008cited by this paper
• The Reacquisition of Biotin Prototrophy in Saccharomyces cerevisiae Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering

  2007influential reference
• Allopatric divergence, secondary contact, and genetic isolation in wild yeast populations.

  2007cited by this paper
• Sequence Diversity, Reproductive Isolation and Species Concepts in Saccharomyces

  2006cited by this paper
• Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution.

  2006cited by this paper
• Genome-wide identification of replication origins in yeast by comparative genomics.

  2006cited by this paper
• The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.

  2005cited by this paper
• Differential effects of leptin administration on the abundance of uncoupling protein-2 and glucocorticoid action during neonatal development

  2005cited by this paper
• Inferences of evolutionary relationships from a population survey of LTR‐retrotransposons and telomeric‐associated sequences in the Saccharomyces sensu stricto complex

  2005cited by this paper
• Automated generation of heuristics for biological sequence comparison

  2005cited by this paper
• Transcriptional regulatory code of a eukaryotic genome

  2004cited by this paper
• Mauve: multiple alignment of conserved genomic sequence with rearrangements.

  2004cited by this paper
• Population Genetics of the Wild Yeast Saccharomyces paradoxus

  2004cited by this paper
• Versatile and open software for comparing large genomes

  2004cited by this paper
• Genome-scale approaches to resolving incongruence in molecular phylogenies

  2003cited by this paper
• Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

  2003influential reference
• Sequencing and comparison of yeast species to identify genes and regulatory elements

  2003influential reference
• Current Protocols in Bioinformatics

  2002cited by this paper
• MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

  2002cited by this paper
• The generic genome browser: a building block for a model organism system database.

  2002cited by this paper
• GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

  2001influential reference
• Pyrosequencing Sheds Light on DNA Sequencing

  2001cited by this paper
• Evolution of gene order in the genomes of two related yeast species.

  2001cited by this paper
• Pyrosequencing sheds light on DNA sequencing.

  2001cited by this paper
• Chromosomal evolution in Saccharomyces

  2000influential reference
• Genomic Exploration of the Hemiascomycetous Yeasts: 5. Saccharomyces bayanus var. uvarum

  2000cited by this paper
• Yeast chromosomes have been significantly reshaped during their evolutionary history.

  2000cited by this paper
• Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae.

  2000cited by this paper
• Tandem repeats finder: a program to analyze DNA sequences.

  1999cited by this paper
• PAML: a program package for phylogenetic analysis by maximum likelihood

  1997cited by this paper
• tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

  1997cited by this paper
• Life with 6000 Genes

  1996influential reference

• Horizontal Transfer and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces

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• Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

  2024cites this paper
• Recombination, admixture and genome instability shape the genomic landscape of Saccharomyces cerevisiae derived from spontaneous grape ferments

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• Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence

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• Unlocking the genome of the non-sourdough Kazachstania humilis MAW1: insights into inhibitory factors and phenotypic properties

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• The genomic landscape of wild Saccharomyces cerevisiae is shaped by complex patterns of admixture, aneuploidy and recombination

  2023cites this paper
• High quality de novo genome assembly of non-conventional yeast Kazachstania bulderi a new potential low pH production host for biorefineries

  2023cites this paper
• Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny

  2023cites this paper
• Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry

  2023cites this paper
• Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces

  2023cites this paper
• Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae

  2022influential citation
• Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

  2022cites this paper
• The Functional Order (FunOrder) tool – Identification of essential biosynthetic genes through computational molecular co-evolution

  2021cites this paper
• A vast evolutionarily transient translatome contributes to phenotype and fitness

  2021cites this paper
• FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution

  2021cites this paper
• Natural Polymorphism of Pectinase PGU Genes in the Saccharomyces Yeasts

  2021cites this paper
• A reference translatome map reveals two modes of protein evolution

  2021cites this paper
• Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes

  2021cites this paper
• Unique Brewing-Relevant Properties of a Strain of Saccharomyces jurei Isolated From Ash (Fraxinus excelsior)

  2021cites this paper
• Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China

  2021cites this paper
• Saccharomyces yeast hybrids on the rise

  2021cites this paper
• Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries

  2021cites this paper
• Vitamin requirements and biosynthesis in Saccharomyces cerevisiae

  2020cites this paper
• Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination

  2020cites this paper
• An update on the diversity, ecology and biogeography of the Saccharomyces genus

  2020cites this paper
• Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae—Phylogeny, Phenotypes, Ecology and Domestication

  2020cites this paper
• Molecular Genetic Features of Biological Species of the Genus Saccharomyces

  2020cites this paper
• Environmental genomics of the Saccharomyces sensu stricto group

  2019cites this paper
• Fermentation innovation through complex hybridization of wild and domesticated yeasts

  2019cites this paper
• Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution

  2019cites this paper
• Saccharomyces Hybrids: Generation And Analysis

  2019cites this paper
• A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae × S. paradoxus Adapted to Olive Brine

  2019cites this paper
• André Goffeau's imprinting on second generation yeast “genomologists”

  2019cites this paper
• Saccharomyces arboricola and Its Hybrids’ Propensity for Sake Production: Interspecific Hybrids Reveal Increased Fermentation Abilities and a Mosaic Metabolic Profile

  2019influential citation
• Interspecific hybridization facilitates niche adaptation in beer yeast

  2019cites this paper
• Genome evolution across 1,011 Saccharomyces cerevisiae isolates

  2018cites this paper
• Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast

  2018cites this paper
• Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei

  2018cites this paper
• sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing

  2018cites this paper
• Interspecies Hybridisation and Genome Chimerisation in Saccharomyces: Combining of Gene Pools of Species and Its Biotechnological Perspectives

  2018cites this paper
• Modeling the contributions of chromosome segregation errors and aneuploidy to Saccharomyces hybrid sterility

  2018cites this paper
• Impact phénotypique des réarrangements chromosomiques et évolution des génomes de levures

  2018cites this paper
• Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication

  2018cites this paper
• Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites

  2017cites this paper
• Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

  2017cites this paper
• Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production

  2017cites this paper
• Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics

  2017cites this paper
• The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the ‘yeast mitochondrial genetic code’

  2017influential citation
• Impact of Chromosomal Translocations (CTs) on reproductive isolation and fitness in natural yeast isolates

  2017cites this paper
• Conceptual and empirical investigations of eukaryotic transposable element evolution

  2017cites this paper
• Contrasting genome dynamics between domesticated and wild yeasts

  2016cites this paper
• Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

  2016cites this paper
• Molecular phylogeny of pectinase genes PGU in the yeast genus Saccharomyces

  2016cites this paper
• Contrasting genome dynamics between domesticated 1 and wild yeasts 2 3

  2016cites this paper
• Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network

  2016cites this paper
• Microbe Domestication and the Identification of the Wild Genetic Stock of Wine Yeasts

  2016cites this paper
• Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae

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• Comparative analysis of sequences, polymorphisms and topology of yeasts aquaporins and aquaglyceroporins.

  2016cites this paper
• Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests.

  2016cites this paper
• Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering

  2016influential citation
• Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection

  2016cites this paper
• Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae

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• XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts

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• Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research

  2016cites this paper
• Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus Group I and II strains.

  2015cites this paper
• Non-paradoxical evolutionary stability of the recombination initiation landscape in Saccharomycetes

  2015cites this paper
• Comparative genomics and transcriptomics in Saccharomyces

  2015cites this paper
• Selection on noise constrains variation in a eukaryotic promoter

  2015cites this paper
• High-Throughput Biochemical Fingerprinting of Saccharomyces cerevisiae by Fourier Transform Infrared Spectroscopy

  2015cites this paper
• Basic principles of yeast genomics, a personal recollection.

  2015cites this paper
• 2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae.

  2015cites this paper
• The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts

  2015cites this paper
• Genomics and the making of yeast biodiversity.

  2015cites this paper
• Genomic Insights into the Saccharomyces sensu stricto Complex

  2015cites this paper
• Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast

  2015cites this paper
• [Genome-wide association study as a method for genetic architecture analysis in polygenic diseases (by the example of multiple sclerosis)].

  2014cites this paper
• A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

  2014cites this paper
• Subtelomeres

  2014cites this paper
• Synteny analysis provides a route to design genus-specific PCR primers for rapid identification of all Saccharomyces species.

  2014cites this paper
• Multiple inputs control sulfur-containing amino acid synthesis in Saccharomyces cerevisiae

  2014cites this paper
• A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum

  2014cites this paper
• Phenotypic characterisation of Saccharomyces spp. yeast for tolerance to stresses encountered during fermentation of lignocellulosic residues to produce bioethanol

  2014cites this paper
• Genomics of Subtelomeres: Technical Problems, Solutions and the Future

  2014cites this paper
• Molecular polymorphism of β-fructosidase SUC genes in the Saccharomyces yeasts

  2014cites this paper
• High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces

  2014cites this paper