Genomic re-assessment of the transposable element landscape of the potato genome

Autores
Zavallo, Diego; Crescente, Juan Manuel; Gantuz, Magdalena; Leone, Melisa; Vanzetti, Leonardo Sebastian; Masuelli, Ricardo Williams; Asurmendi, Sebastian
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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, 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.
Instituto de Biotecnología
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
Plant Cell Reports 39 : 1161–1174 (2020)
Materia
Papa
Genética
Transposones
Solanum tuberosum
Potatoes
Transposons
Genetics
Elementos Genéticos Transponibles
Transposable Element
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/7754
Acceder
id INTADig_d61bcd0c73d2950c1538811b47f6a929
oai_identifier_str oai:localhost:20.500.12123/7754
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling Genomic re-assessment of the transposable element landscape of the potato genomeZavallo, DiegoCrescente, Juan ManuelGantuz, MagdalenaLeone, MelisaVanzetti, Leonardo SebastianMasuelli, Ricardo WilliamsAsurmendi, SebastianPapaGenéticaTransposonesSolanum tuberosumPotatoesTransposonsGeneticsElementos Genéticos TransponiblesTransposable ElementTransposable 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.Instituto de BiotecnologíaFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: 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; ArgentinaFil: 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; ArgentinaFil: 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; ArgentinaFil: 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; ArgentinaFil: 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; ArgentinaFil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaSpringer2020-08-21T13:25:40Z2020-08-21T13:25:40Z2020-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/7754https://link.springer.com/article/10.1007/s00299-020-02554-80721-77141432-203Xhttps://doi.org/10.1007/s00299-020-02554-8Plant Cell Reports 39 : 1161–1174 (2020)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-09-04T09:48:36Zoai:localhost:20.500.12123/7754instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:48:37.001INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Genomic re-assessment of the transposable element landscape of the potato genome
title Genomic re-assessment of the transposable element landscape of the potato genome
spellingShingle Genomic re-assessment of the transposable element landscape of the potato genome
Zavallo, Diego
Papa
Genética
Transposones
Solanum tuberosum
Potatoes
Transposons
Genetics
Elementos Genéticos Transponibles
Transposable Element
title_short Genomic re-assessment of the transposable element landscape of the potato genome
title_full Genomic re-assessment of the transposable element landscape of the potato genome
title_fullStr Genomic re-assessment of the transposable element landscape of the potato genome
title_full_unstemmed Genomic re-assessment of the transposable element landscape of the potato genome
title_sort Genomic re-assessment of the transposable element landscape of the potato genome
dc.creator.none.fl_str_mv Zavallo, Diego
Crescente, Juan Manuel
Gantuz, Magdalena
Leone, Melisa
Vanzetti, Leonardo Sebastian
Masuelli, Ricardo Williams
Asurmendi, Sebastian
author Zavallo, Diego
author_facet Zavallo, Diego
Crescente, Juan Manuel
Gantuz, Magdalena
Leone, Melisa
Vanzetti, Leonardo Sebastian
Masuelli, Ricardo Williams
Asurmendi, Sebastian
author_role author
author2 Crescente, Juan Manuel
Gantuz, Magdalena
Leone, Melisa
Vanzetti, Leonardo Sebastian
Masuelli, Ricardo Williams
Asurmendi, Sebastian
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Papa
Genética
Transposones
Solanum tuberosum
Potatoes
Transposons
Genetics
Elementos Genéticos Transponibles
Transposable Element
topic Papa
Genética
Transposones
Solanum tuberosum
Potatoes
Transposons
Genetics
Elementos Genéticos Transponibles
Transposable Element
dc.description.none.fl_txt_mv 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, 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.
Instituto de Biotecnología
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: 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; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description 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, 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.
publishDate 2020
dc.date.none.fl_str_mv 2020-08-21T13:25:40Z
2020-08-21T13:25:40Z
2020-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/7754
https://link.springer.com/article/10.1007/s00299-020-02554-8
0721-7714
1432-203X
https://doi.org/10.1007/s00299-020-02554-8
url http://hdl.handle.net/20.500.12123/7754
https://link.springer.com/article/10.1007/s00299-020-02554-8
https://doi.org/10.1007/s00299-020-02554-8
identifier_str_mv 0721-7714
1432-203X
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv Plant Cell Reports 39 : 1161–1174 (2020)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
_version_ 1842341380540596224
score 12.623145

Publicaciones similares