Transposable elements versus the fungal genome: impact on whole-genome architecture and transcriptional profiles

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dc.contributor.authorCastanera Andrés, Raúl
dc.contributor.authorLópez Varas, Leticia
dc.contributor.authorBorgognone, Alessandra
dc.contributor.authorLaButti, Kurt
dc.contributor.authorLapidus, Alla
dc.contributor.authorSchmutz, Jeremy
dc.contributor.authorGrimwood, Jane
dc.contributor.authorPérez Garrido, María Gumersinda
dc.contributor.authorPisabarro de Lucas, Gerardo
dc.contributor.authorGrigoriev, Igor V.
dc.contributor.authorStajich, Jason E.
dc.contributor.authorRamírez Nasto, Lucía
dc.contributor.departmentProducción Agrariaes_ES
dc.contributor.departmentNekazaritza Ekoizpenaeu
dc.date.accessioned2017-12-11T11:43:02Z
dc.date.available2017-12-11T11:43:02Z
dc.date.issued2016
dc.descriptionIncluye 10 ficheros de datoses_ES
dc.description.abstractTransposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.en
dc.description.sponsorshipThis work was supported by Spanish National Research Plan (Projects AGL2011-30495 and AGL2014-55971-R) and FEDER funds; Public University of Navarre; U.S. Department of Energy Joint Genome Institute; and Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Ten
dc.format.mimetypeapplication/pdfen
dc.format.mimetypeapplication/zipen
dc.identifier.doi10.1371/journal.pgen.1006108
dc.identifier.issn1553-7390 (Print)
dc.identifier.issn1553-7404 (Electronic)
dc.identifier.urihttps://academica-e.unavarra.es/handle/2454/26508
dc.language.isoengen
dc.publisherPublic Library of Scienceen
dc.relation.ispartofPLoS Genetics 12(6):e1006108en
dc.relation.projectIDinfo:eu-repo/grantAgreement/ES/6PN/AGL2011-300495/
dc.relation.projectIDinfo:eu-repo/grantAgreement/MINECO//AGL2014-55971-R/ES/
dc.relation.publisherversionhttps://doi.org/10.1371/journal.pgen.1006108
dc.rightsThis is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.en
dc.rights.accessRightsinfo:eu-repo/semantics/openAccess
dc.rights.urihttps://creativecommons.org/publicdomain/zero/1.0/
dc.subjectTransposable elementsen
dc.subjectFungal genomeen
dc.titleTransposable elements versus the fungal genome: impact on whole-genome architecture and transcriptional profilesen
dc.typeinfo:eu-repo/semantics/article
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dspace.entity.typePublication
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relation.isAuthorOfPublication.latestForDiscovery37776e2e-4a19-49fa-86d2-8691c240f2ad

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