Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic

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dc.contributor.authorMarcon, Helena Sanches [UNESP]
dc.contributor.authorDomingues, Douglas Silva [UNESP]
dc.contributor.authorSilva, Juliana Costa
dc.contributor.authorBorges, Rafael Junqueira [UNESP]
dc.contributor.authorMatioli, Fábio Filippi [UNESP]
dc.contributor.authorFontes, Marcos Roberto de Mattos [UNESP]
dc.contributor.authorMarino, Celso Luis [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionInstituto Agronômico do Paraná (IAPAR)
dc.date.accessioned2015-12-07T15:36:58Z
dc.date.available2015-12-07T15:36:58Z
dc.date.issued2015-08-14
dc.description.abstractIn Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome. We characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one Copia family, RLC_egBianca_1. Protein theoretical models suggest different properties between Copia and Gypsy domains. IRAP and REMAP markers suggested genomic polymorphisms among Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values. Our strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.en
dc.description.affiliationDepartamento de Genética, Instituto de Biociências de Botucatu (IBB), Universidade Estadual Paulista (UNESP), Botucatu, SP, Brasil
dc.description.affiliationPrograma de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista (UNESP), Botucatu, SP, Brasil
dc.description.affiliationDepartamento de Botânica, Instituto de Biociências de Rio Claro (IBRC), Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brasil
dc.description.affiliationPlant Biotechnology Laboratory, Instituto Agronômico do Paraná (IAPAR), Londrina, PR, Brasil
dc.description.affiliationDepartamento de Física e Biofísica, Instituto de Biociências de Botucatu (IBB), Universidade Estadual Paulista (UNESP), Botucatu, SP, Brasil, INCTTOX-CNPq, Brasil
dc.description.affiliationInstituto de Biotecnologia (IBTEC), Universidade Estadual Paulista (UNESP), Botucatu, SP, Brasil
dc.description.affiliationUnespUniversidade Estadual Paulista, Departamento de Genética, Instituto de Biociências de Botucatu
dc.description.affiliationUnespUniversidade Estadual Paulista, Departamento de Botânica, Instituto de Biociências de Rio Claro
dc.description.affiliationUnespUniversidade Estadual Paulista, Departamento de Física e Biofísica, Instituto de Biociências de Botucatu
dc.description.affiliationUnespUniversidade Estadual Paulista, Instituto de Biotecnologia de Botucatu
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
dc.description.sponsorshipCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
dc.description.sponsorshipIdCNPq: 474123/2010-3
dc.format.extent198-213
dc.identifierhttp://dx.doi.org/10.1186/s12870-015-0550-1
dc.identifier.citationBMC Plant Biology, v. 15, p. 198-213, 2015.
dc.identifier.doi10.1186/s12870-015-0550-1
dc.identifier.filePMC4535378.pdf
dc.identifier.issn1471-2229
dc.identifier.lattes4320362411241786
dc.identifier.lattes0165348738208319
dc.identifier.orcid0000-0003-4524-954X
dc.identifier.pmcPMC4535378
dc.identifier.pubmed26268941
dc.identifier.urihttp://hdl.handle.net/11449/131524
dc.language.isoeng
dc.publisherBioMed Central
dc.relation.ispartofBMC Plant Biology
dc.relation.ispartofjcr3.930
dc.relation.ispartofsjr1,887
dc.rights.accessRightsAcesso aberto
dc.sourcePubMed
dc.subjectLTR retrotransposonsen
dc.subjectDynamicsen
dc.subjectGenomic distributionen
dc.subjectComparative analysisen
dc.subjectEucalyptus genomesen
dc.titleTranscriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphicen
dc.typeArtigo
dcterms.rightsHolderBioMed Central LTD
unesp.author.lattes4320362411241786
unesp.author.lattes0165348738208319[7]
unesp.author.orcid0000-0003-4524-954X[7]
unesp.campusUniversidade Estadual Paulista (Unesp), Instituto de Biociências, Botucatupt
unesp.campusUniversidade Estadual Paulista (Unesp), Instituto de Biociências, Rio Claropt

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Artigos - Genética - IBB
Artigos - Botânica - IBRC
Artigos - Física e Biofísica - IBB