Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.

Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years...

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Autores principales:	Martin Carr, Douda Bensasson, Casey M Bergman
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/62be35660ead4d1e9f237ffb7ec9d57f
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spelling	oai:doaj.org-article:62be35660ead4d1e9f237ffb7ec9d57f2021-11-18T08:06:37ZEvolutionary genomics of transposable elements in Saccharomyces cerevisiae.1932-620310.1371/journal.pone.0050978https://doaj.org/article/62be35660ead4d1e9f237ffb7ec9d57f2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23226439/?tool=EBIhttps://doaj.org/toc/1932-6203Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of all Ty families in S. cerevisiae based on a systematic re-annotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the genomic diversity of transposable elements in unicellular eukaryotes.Martin CarrDouda BensassonCasey M BergmanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e50978 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Martin Carr Douda Bensasson Casey M Bergman Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
description	Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of all Ty families in S. cerevisiae based on a systematic re-annotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the genomic diversity of transposable elements in unicellular eukaryotes.
format	article
author	Martin Carr Douda Bensasson Casey M Bergman
author_facet	Martin Carr Douda Bensasson Casey M Bergman
author_sort	Martin Carr
title	Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
title_short	Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
title_full	Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
title_fullStr	Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
title_full_unstemmed	Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
title_sort	evolutionary genomics of transposable elements in saccharomyces cerevisiae.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/62be35660ead4d1e9f237ffb7ec9d57f
work_keys_str_mv	AT martincarr evolutionarygenomicsoftransposableelementsinsaccharomycescerevisiae AT doudabensasson evolutionarygenomicsoftransposableelementsinsaccharomycescerevisiae AT caseymbergman evolutionarygenomicsoftransposableelementsinsaccharomycescerevisiae
_version_	1718422231145512960

Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.

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