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Genome-wide analysis of intraspecific transposon diversity in yeast

BACKGROUND: In the model organism Saccharomyces cerevisiae, the transposable elements (TEs) consist of LTR (Long Terminal Repeat) retrotransposons called Ty elements belonging to five families, Ty1 to Ty5. They take the form of either full-length coding elements or non-coding solo-LTRs corresponding...

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Autores principales: Bleykasten-Grosshans, Claudine, Friedrich, Anne, Schacherer, Joseph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022208/
https://www.ncbi.nlm.nih.gov/pubmed/23768249
http://dx.doi.org/10.1186/1471-2164-14-399
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author Bleykasten-Grosshans, Claudine
Friedrich, Anne
Schacherer, Joseph
author_facet Bleykasten-Grosshans, Claudine
Friedrich, Anne
Schacherer, Joseph
author_sort Bleykasten-Grosshans, Claudine
collection PubMed
description BACKGROUND: In the model organism Saccharomyces cerevisiae, the transposable elements (TEs) consist of LTR (Long Terminal Repeat) retrotransposons called Ty elements belonging to five families, Ty1 to Ty5. They take the form of either full-length coding elements or non-coding solo-LTRs corresponding to remnants of former transposition events. Although the biological features of Ty elements have been studied in detail in S. cerevisiae and the Ty content of the reference strain (S288c) was accurately annotated, the Ty-related intra-specific diversity has not been closely investigated so far. RESULTS: In this study, we investigated the Ty contents of 41 available genomes of isolated S. cerevisiae strains of diverse geographical and ecological origins. The strains were compared in terms of the number of Ty copies, the content of the potential transpositionally active elements and the genomic insertion maps. The strain repertoires were also investigated in the closely related Ty1 and Ty2 families and subfamilies. CONCLUSIONS: This is the first genome-wide analysis of the diversity associated to the Ty elements, carried out for a large set of S. cerevisiae strains. The results of the present analyses suggest that the current Ty-related polymorphism has resulted from multiple causes such as differences between strains, between Ty families and over time, in the recent transpositional activity of Ty elements. Some new Ty1 variants were also identified, and we have established that Ty1 variants have different patterns of distribution among strains, which further contributes to the strain diversity.
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spelling pubmed-40222082014-05-16 Genome-wide analysis of intraspecific transposon diversity in yeast Bleykasten-Grosshans, Claudine Friedrich, Anne Schacherer, Joseph BMC Genomics Research Article BACKGROUND: In the model organism Saccharomyces cerevisiae, the transposable elements (TEs) consist of LTR (Long Terminal Repeat) retrotransposons called Ty elements belonging to five families, Ty1 to Ty5. They take the form of either full-length coding elements or non-coding solo-LTRs corresponding to remnants of former transposition events. Although the biological features of Ty elements have been studied in detail in S. cerevisiae and the Ty content of the reference strain (S288c) was accurately annotated, the Ty-related intra-specific diversity has not been closely investigated so far. RESULTS: In this study, we investigated the Ty contents of 41 available genomes of isolated S. cerevisiae strains of diverse geographical and ecological origins. The strains were compared in terms of the number of Ty copies, the content of the potential transpositionally active elements and the genomic insertion maps. The strain repertoires were also investigated in the closely related Ty1 and Ty2 families and subfamilies. CONCLUSIONS: This is the first genome-wide analysis of the diversity associated to the Ty elements, carried out for a large set of S. cerevisiae strains. The results of the present analyses suggest that the current Ty-related polymorphism has resulted from multiple causes such as differences between strains, between Ty families and over time, in the recent transpositional activity of Ty elements. Some new Ty1 variants were also identified, and we have established that Ty1 variants have different patterns of distribution among strains, which further contributes to the strain diversity. BioMed Central 2013-06-14 /pmc/articles/PMC4022208/ /pubmed/23768249 http://dx.doi.org/10.1186/1471-2164-14-399 Text en Copyright © 2013 Bleykasten-Grosshans et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Bleykasten-Grosshans, Claudine
Friedrich, Anne
Schacherer, Joseph
Genome-wide analysis of intraspecific transposon diversity in yeast
title Genome-wide analysis of intraspecific transposon diversity in yeast
title_full Genome-wide analysis of intraspecific transposon diversity in yeast
title_fullStr Genome-wide analysis of intraspecific transposon diversity in yeast
title_full_unstemmed Genome-wide analysis of intraspecific transposon diversity in yeast
title_short Genome-wide analysis of intraspecific transposon diversity in yeast
title_sort genome-wide analysis of intraspecific transposon diversity in yeast
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022208/
https://www.ncbi.nlm.nih.gov/pubmed/23768249
http://dx.doi.org/10.1186/1471-2164-14-399
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