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Abstract
Transposable elements (TEs) are DNA sequences with the ability to autoreplicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, [ver mas...]
dc.contributor.authorZavallo, Diego
dc.contributor.authorCrescente, Juan Manuel
dc.contributor.authorGantuz, Magdalena
dc.contributor.authorLeone, Melisa
dc.contributor.authorVanzetti, Leonardo Sebastian
dc.contributor.authorMasuelli, Ricardo Williams
dc.contributor.authorAsurmendi, Sebastian
dc.date.accessioned2020-08-21T13:25:40Z
dc.date.available2020-08-21T13:25:40Z
dc.date.issued2020-05
dc.identifier.issn0721-7714
dc.identifier.issn1432-203X
dc.identifier.otherhttps://doi.org/10.1007/s00299-020-02554-8
dc.identifier.urihttp://hdl.handle.net/20.500.12123/7754
dc.identifier.urihttps://link.springer.com/article/10.1007/s00299-020-02554-8
dc.description.abstractTransposable elements (TEs) are DNA sequences with the ability to autoreplicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification and annotation through an open-source and freely available pipeline (https://github.com/DiegoZavallo/TE_Discovery). Using a variety of tools, approaches and rules, we were able to provide a clearly annotated of characterized TEs landscape. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies. While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all the necessary steps to perform de novo detection for other species.eng
dc.formatapplication/pdfes_AR
dc.language.isoenges_AR
dc.publisherSpringeres_AR
dc.rightsinfo:eu-repo/semantics/restrictedAccesses_AR
dc.sourcePlant Cell Reports 39 : 1161–1174 (2020)es_AR
dc.subjectPapaes_AR
dc.subjectPotatoeseng
dc.subjectGenéticaes_AR
dc.subjectTransposoneses_AR
dc.subjectTransposonseng
dc.subjectSolanum tuberosumes_AR
dc.subjectGeneticseng
dc.subject.otherElementos Genéticos Transponibles
dc.subject.otherTransposable Elementeng
dc.titleGenomic re-assessment of the transposable element landscape of the potato genomees_AR
dc.typeinfo:ar-repo/semantics/artículoes_AR
dc.typeinfo:eu-repo/semantics/articlees_AR
dc.typeinfo:eu-repo/semantics/publishedVersiones_AR
dc.description.origenInstituto de Biotecnologíaes_AR
dc.description.filFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Gantuz, Magdalena. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza (IBAM). Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Agrícola de Mendoza; Argentinaes_AR
dc.description.filFil: Leone, Melisa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Agencia Nacional de Promocion Científica y Tecnológica; Argentinaes_AR
dc.description.filFil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Masuelli, Ricardo Williams. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza (IBAM). Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Agrícola de Mendoza; Argentinaes_AR
dc.description.filFil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.subtypecientifico


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