Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.

<h4>Background</h4>The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterize...

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Autores principales:	Jessy Labbé, Claude Murat, Emmanuelle Morin, Gerald A Tuskan, François Le Tacon, Francis Martin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b00e1a3942dd45bf98b2abac4240e19a
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spelling	oai:doaj.org-article:b00e1a3942dd45bf98b2abac4240e19a2021-11-18T07:09:54ZCharacterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.1932-620310.1371/journal.pone.0040197https://doaj.org/article/b00e1a3942dd45bf98b2abac4240e19a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22870194/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome.<h4>Methodology/principal findings</h4>TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea.<h4>Conclusions</h4>This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.Jessy LabbéClaude MuratEmmanuelle MorinGerald A TuskanFrançois Le TaconFrancis MartinPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e40197 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jessy Labbé Claude Murat Emmanuelle Morin Gerald A Tuskan François Le Tacon Francis Martin Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.
description	<h4>Background</h4>The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome.<h4>Methodology/principal findings</h4>TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea.<h4>Conclusions</h4>This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.
format	article
author	Jessy Labbé Claude Murat Emmanuelle Morin Gerald A Tuskan François Le Tacon Francis Martin
author_facet	Jessy Labbé Claude Murat Emmanuelle Morin Gerald A Tuskan François Le Tacon Francis Martin
author_sort	Jessy Labbé
title	Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.
title_short	Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.
title_full	Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.
title_fullStr	Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.
title_full_unstemmed	Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.
title_sort	characterization of transposable elements in the ectomycorrhizal fungus laccaria bicolor.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/b00e1a3942dd45bf98b2abac4240e19a
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Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.

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