Genomic re-assessment of the transposable element landscape of the potato genome
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 s...
| Autores principales: | , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2020
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| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855484068824612864 |
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| author | Zavallo, Diego Crescente, Juan Manuel Gantuz, Magdalena Leone, Melisa Vanzetti, Leonardo Sebastian Masuelli, Ricardo Williams Asurmendi, Sebastian |
| author_browse | Asurmendi, Sebastian Crescente, Juan Manuel Gantuz, Magdalena Leone, Melisa Masuelli, Ricardo Williams Vanzetti, Leonardo Sebastian Zavallo, Diego |
| author_facet | Zavallo, Diego Crescente, Juan Manuel Gantuz, Magdalena Leone, Melisa Vanzetti, Leonardo Sebastian Masuelli, Ricardo Williams Asurmendi, Sebastian |
| author_sort | Zavallo, Diego |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA7754 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA77542020-08-21T13:32:41Z Genomic re-assessment of the transposable element landscape of the potato genome Zavallo, Diego Crescente, Juan Manuel Gantuz, Magdalena Leone, Melisa Vanzetti, Leonardo Sebastian Masuelli, Ricardo Williams Asurmendi, Sebastian Papa Genética Transposones Solanum tuberosum Potatoes Transposons Genetics Elementos Genéticos Transponibles Transposable Element 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 2020-08-21T13:25:40Z 2020-08-21T13:25:40Z 2020-05 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng info:eu-repo/semantics/restrictedAccess application/pdf Springer Plant Cell Reports 39 : 1161–1174 (2020) |
| spellingShingle | Papa Genética Transposones Solanum tuberosum Potatoes Transposons Genetics Elementos Genéticos Transponibles Transposable Element Zavallo, Diego Crescente, Juan Manuel Gantuz, Magdalena Leone, Melisa Vanzetti, Leonardo Sebastian Masuelli, Ricardo Williams Asurmendi, Sebastian 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 |
| 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_short | 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 |
| topic | Papa Genética Transposones Solanum tuberosum Potatoes Transposons Genetics Elementos Genéticos Transponibles Transposable Element |
| 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 |
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