Publicação
Transcriptome variability in yeast strains
| Resumo: | In order to understand yeast natural genome and transcriptome variability and evaluate whether such variability correlates with phenotypic diversity, we have isolated approximately 1000 yeast strains from Portuguese vineyards, namely from the Bairrada and Minho wine regions, genotyped them and selected the most divergent ones for genome and transcriptome characterization, using comparative genome hybridization on array (aCGH) and mRNA profiling, respectively. For comparative purposes, strains isolated from opportunistic clinical infections and commercial strains used by the wine industry were also included in the study. Approximately 3 % of the ORFeome showed copy number alterations relative to the reference strain S288C, which was associated with sub-telomeric instability and Ty element transposition. Interestingly, one third of the Ty elements identified in the genome of the reference laboratory strain (S288C) were absent in the wine strains, but were present in the clinical isolates. Distinct gene functional classes were affected by copy number changes in wine and clinical strains. However, no correlation was found between genome alterations and geographical origin. Transcriptome profiling of the same strains grown in synthetic must, using a common reference design, showed important variation in mRNA levels during fermentation, in particular in the wine isolates. Some genes showed patterns of activation that were consistent with gene copy number differences, while others pointed to strain specific regulation. Substantial variability in expression levels were detected among genes associated with fermentation in the wine strains. Therefore, transcriptome variability is relevant to understand yeast adaptation to new ecological niches, yeast evolution, and also to design strategies to select strains with particular phenotypes. |
|---|---|
| Autores principais: | Carreto, Laura |
| Outros Autores: | Schuller, Dorit Elisabeth; Santos, Manuel A. S. |
| Assunto: | Genome variability Transcriptome variability Saccharomyces cerevisiae Comparative genome hybridization on array mRNA profiling Clinical infections Natural isolates |
| Ano: | 2008 |
| País: | Portugal |
| Tipo de documento: | póster em conferência |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| _version_ | 1877775406482849792 |
|---|---|
| author | Carreto, Laura |
| author2 | Schuller, Dorit Elisabeth Santos, Manuel A. S. |
| author2_role | author author |
| author_facet | Carreto, Laura Schuller, Dorit Elisabeth Santos, Manuel A. S. |
| author_role | author |
| contributor_name_str_mv | RepositóriUM - Universidade do Minho |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Carreto, Laura\"},{\"Person.name\":\"Schuller, Dorit Elisabeth\"},{\"Person.name\":\"Santos, Manuel A. S.\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | RepositóriUM - Universidade do Minho |
| datacite.creators.creator.creatorName.fl_str_mv | Carreto, Laura Schuller, Dorit Elisabeth Santos, Manuel A. S. |
| datacite.date.Accepted.fl_str_mv | 2008-10-01T00:00:00Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | Genome variability Transcriptome variability Saccharomyces cerevisiae Comparative genome hybridization on array mRNA profiling Clinical infections Natural isolates |
| datacite.titles.title.fl_str_mv | Transcriptome variability in yeast strains |
| dc.contributor.none.fl_str_mv | RepositóriUM - Universidade do Minho |
| dc.creator.none.fl_str_mv | Carreto, Laura Schuller, Dorit Elisabeth Santos, Manuel A. S. |
| dc.date.Accepted.fl_str_mv | 2008-10-01T00:00:00Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | https://hdl.handle.net/1822/11604 |
| dc.language.none.fl_str_mv | eng |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.subject.none.fl_str_mv | Genome variability Transcriptome variability Saccharomyces cerevisiae Comparative genome hybridization on array mRNA profiling Clinical infections Natural isolates |
| dc.title.fl_str_mv | Transcriptome variability in yeast strains |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_6670 |
| description | In order to understand yeast natural genome and transcriptome variability and evaluate whether such variability correlates with phenotypic diversity, we have isolated approximately 1000 yeast strains from Portuguese vineyards, namely from the Bairrada and Minho wine regions, genotyped them and selected the most divergent ones for genome and transcriptome characterization, using comparative genome hybridization on array (aCGH) and mRNA profiling, respectively. For comparative purposes, strains isolated from opportunistic clinical infections and commercial strains used by the wine industry were also included in the study. Approximately 3 % of the ORFeome showed copy number alterations relative to the reference strain S288C, which was associated with sub-telomeric instability and Ty element transposition. Interestingly, one third of the Ty elements identified in the genome of the reference laboratory strain (S288C) were absent in the wine strains, but were present in the clinical isolates. Distinct gene functional classes were affected by copy number changes in wine and clinical strains. However, no correlation was found between genome alterations and geographical origin. Transcriptome profiling of the same strains grown in synthetic must, using a common reference design, showed important variation in mRNA levels during fermentation, in particular in the wine isolates. Some genes showed patterns of activation that were consistent with gene copy number differences, while others pointed to strain specific regulation. Substantial variability in expression levels were detected among genes associated with fermentation in the wine strains. Therefore, transcriptome variability is relevant to understand yeast adaptation to new ecological niches, yeast evolution, and also to design strategies to select strains with particular phenotypes. |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | conferencePoster |
| id | rum_2ea4e138db382cfef68fb7c4441d3920 |
| identifier.url.fl_str_mv | https://hdl.handle.net/1822/11604 |
| inst_facet_str | urn:organizationAcronym:repositorium{{{_:::_}}}Universidade do Minho |
| instacron_str | repositorium |
| institution | Universidade do Minho |
| instname_str | Universidade do Minho |
| language | eng |
| network_acronym_str | rum |
| network_name_str | RepositóriUM - Universidade do Minho |
| oai_identifier_str | oai:repositorium.uminho.pt:1822/11604 |
| organization_str_mv | urn:organizationAcronym:repositorium |
| person_str_mv | Carreto, Laura Schuller, Dorit Elisabeth Santos, Manuel A. S. |
| publishDate | 2008 |
| repo_facet_str | urn:repositoryAcronym:rum{{{_:::_}}}RepositóriUM - Universidade do Minho |
| reponame_str | RepositóriUM - Universidade do Minho |
| repository_id_str | urn:repositoryAcronym:rum |
| service_str_mv | urn:repositoryAcronym:rum |
| spelling | engporIn order to understand yeast natural genome and transcriptome variability and evaluate whether such variability correlates with phenotypic diversity, we have isolated approximately 1000 yeast strains from Portuguese vineyards, namely from the Bairrada and Minho wine regions, genotyped them and selected the most divergent ones for genome and transcriptome characterization, using comparative genome hybridization on array (aCGH) and mRNA profiling, respectively. For comparative purposes, strains isolated from opportunistic clinical infections and commercial strains used by the wine industry were also included in the study. Approximately 3 % of the ORFeome showed copy number alterations relative to the reference strain S288C, which was associated with sub-telomeric instability and Ty element transposition. Interestingly, one third of the Ty elements identified in the genome of the reference laboratory strain (S288C) were absent in the wine strains, but were present in the clinical isolates. Distinct gene functional classes were affected by copy number changes in wine and clinical strains. However, no correlation was found between genome alterations and geographical origin. Transcriptome profiling of the same strains grown in synthetic must, using a common reference design, showed important variation in mRNA levels during fermentation, in particular in the wine isolates. Some genes showed patterns of activation that were consistent with gene copy number differences, while others pointed to strain specific regulation. Substantial variability in expression levels were detected among genes associated with fermentation in the wine strains. Therefore, transcriptome variability is relevant to understand yeast adaptation to new ecological niches, yeast evolution, and also to design strategies to select strains with particular phenotypes.application/pdfporTranscriptome variability in yeast strainsCarreto, LauraSchuller, Dorit ElisabethSantos, Manuel A. S.HostingInstitutionOrganizationalRepositóriUM - Universidade do Minhoe-mailmailto:repositorium@usdb.uminho.ptrepositorium@usdb.uminho.ptCITATIONWORKSHOP ON EVOLUTIONARY AND ENVIRONMENTAL GENOMICS OF YEASTS, Heidelberg, 2008 - “Workshop on Evolutionary and Environmental Genomics of Yeasts”. [S.l. : European Molecular Biology Laboratory, 2008].2008-102008-10-01T00:00:00ZHandlehttps://hdl.handle.net/1822/11604http://purl.org/coar/access_right/c_abf2open accessGenome variabilityTranscriptome variabilitySaccharomyces cerevisiaeComparative genome hybridization on arraymRNA profilingClinical infectionsNatural isolates138980 bytesother research producthttp://purl.org/coar/resource_type/c_6670conference posterhttp://purl.org/coar/access_right/c_abf2application/pdfhttps://repositorium.uminho.pt/bitstreams/5ad34a04-1ccc-43a2-bf51-0c9503397021/download |
| spellingShingle | Transcriptome variability in yeast strains Carreto, Laura Genome variability Transcriptome variability Saccharomyces cerevisiae Comparative genome hybridization on array mRNA profiling Clinical infections Natural isolates |
| status | SINGLETON |
| subject.fl_str_mv | Genome variability Transcriptome variability Saccharomyces cerevisiae Comparative genome hybridization on array mRNA profiling Clinical infections Natural isolates |
| title | Transcriptome variability in yeast strains |
| title_full | Transcriptome variability in yeast strains |
| title_fullStr | Transcriptome variability in yeast strains |
| title_full_unstemmed | Transcriptome variability in yeast strains |
| title_short | Transcriptome variability in yeast strains |
| title_sort | Transcriptome variability in yeast strains |
| topic | Genome variability Transcriptome variability Saccharomyces cerevisiae Comparative genome hybridization on array mRNA profiling Clinical infections Natural isolates |
| topic_facet | Genome variability Transcriptome variability Saccharomyces cerevisiae Comparative genome hybridization on array mRNA profiling Clinical infections Natural isolates |
| url | https://hdl.handle.net/1822/11604 |
| visible | 1 |
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