Into the wild: new yeast genomes from natural environments and new tools for their analysis

ABSTRACT Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important speci...

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Published inFEMS yeast research Vol. 20; no. 2; pp. 1 - 15
Main Authors Libkind, D, Peris, D, Cubillos, F A, Steenwyk, J L, Opulente, D A, Langdon, Q K, Rokas, A, Hittinger, C T
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.03.2020
Subjects
Animal behavior
Ascomycota - genetics
BASIC BIOLOGICAL SCIENCES
Basidiomycota - genetics
Biotechnological microorganisms
Biotechnology
Chromosome Mapping
Computational Biology - methods
Domestication
Environment
Fermentation
Genome, Fungal
Genomes
Genomics
Hanseniaspora
Hanseniaspora - genetics
High-Throughput Nucleotide Sequencing
Microbial biotechnology
Mini Review
Minireview
Next-generation sequencing
Phaffia
Saccharomyces
Saccharomyces - genetics
Wild yeast
Wine - analysis
Yeast
Yeasts - classification
Yeasts - genetics
China
Phaffia
Hanseniaspora
Wild yeast
Biotechnology
Saccharomyces
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Abstract ABSTRACT Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts. New genome sequencing technologies together with new bioinformatic tools provide unique insights into the fascinating stories of wild and non-conventional yeast.
AbstractList Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts. Keywords: Saccharomyces; Hanseniaspora; Phaffia; Biotechnology; Wild yeast
ABSTRACT Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts. New genome sequencing technologies together with new bioinformatic tools provide unique insights into the fascinating stories of wild and non-conventional yeast.
Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora ) and Basidiomycota (e.g. Phaffia ). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts. New genome sequencing technologies together with new bioinformatic tools provide unique insights into the fascinating stories of wild and non-conventional yeast.
Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
ABSTRACT Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
Genomic studies of yeasts from the wild have increased significantly in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. Furthermore, we assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
Audience Academic
Author Libkind, D
Peris, D
Hittinger, C T
Steenwyk, J L
Langdon, Q K
Cubillos, F A
Rokas, A
Opulente, D A
AuthorAffiliation 4 Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología. Alameda 3363 . Estación Central. Santiago , Chile
2 Department of Food Biotechnology, Institute of Agrochemistry and Food Technology-CSIC, Calle Catedrático Dr. D. Agustin Escardino Benlloch n°7, 46980 Paterna, Valencia , Spain
5 Department of Biological Sciences, VU Station B#35-1634, Vanderbilt University, Nashville, TN 37235 , USA
6 Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI 53726-4084 , USA
1 Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET/Universidad Nacional del Comahue, Quintral 1250 , Bariloche. , Argentina
3 Millennium Institute for Integrative Biology (iBio). General del Canto 51 , Santiago
7 DOE Great Lakes Bioenergy
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/32009143$$D View this record in MEDLINE/PubMed
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IEDL.DBID RPM
ISSN 1567-1356
IngestDate Tue Sep 17 20:57:56 EDT 2024
Fri May 19 00:41:50 EDT 2023
Sat Oct 26 00:35:03 EDT 2024
Mon Nov 04 11:28:52 EST 2024
Thu Feb 22 23:47:23 EST 2024
Tue Nov 12 23:22:12 EST 2024
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IsDoiOpenAccess true
IsOpenAccess true
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IsScholarly true
Issue 2
Keywords Phaffia
Hanseniaspora
Wild yeast
Biotechnology
Saccharomyces
Language English
License This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)
FEMS 2020.
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Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
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content type line 23
ObjectType-Review-2
National Scientific and Technical Research Council
SC0018409; DEB-1442148; PIP11220130100392CO
National Science Foundation (NSF)
USDA National Institute of Food and Agriculture
USDOE Office of Science (SC), Biological and Environmental Research (BER)
ORCID 0000-0002-7248-6551
0000-0001-9687-6186
0000-0001-5088-7461
0000-0002-8436-595X
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OpenAccessLink https://www.osti.gov/servlets/purl/1600974
PMID 32009143
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PQPubID 2044077
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PublicationTitle FEMS yeast research
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Snippet ABSTRACT Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in...
Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput...
Genomic studies of yeasts from the wild have increased significantly in the past few years. This revolution has been fueled by advances in high-throughput...
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SubjectTerms Animal behavior
Ascomycota - genetics
BASIC BIOLOGICAL SCIENCES
Basidiomycota - genetics
Biotechnological microorganisms
Biotechnology
Chromosome Mapping
Computational Biology - methods
Domestication
Environment
Fermentation
Genome, Fungal
Genomes
Genomics
Hanseniaspora
Hanseniaspora - genetics
High-Throughput Nucleotide Sequencing
Microbial biotechnology
Mini Review
Minireview
Next-generation sequencing
Phaffia
Saccharomyces
Saccharomyces - genetics
Wild yeast
Wine - analysis
Yeast
Yeasts - classification
Yeasts - genetics
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Title Into the wild: new yeast genomes from natural environments and new tools for their analysis
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Volume 20
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