New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing
Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | info:ar-repo/semantics/artículo |
| Language: | Inglés |
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2017
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| Online Access: | http://hdl.handle.net/20.500.12123/1142 https://www.sciencedirect.com/science/article/pii/S016894521400291X?via%3Dihub https://doi.org/10.1016/j.plantsci.2014.12.004 |
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| author | Helguera, Marcelo Rivarola, Maximo Lisandro Clavijo, Bernardo Martis, Mihaela M. Vanzetti, Leonardo Sebastian Gonzalez, Sergio Alberto Garbus, Ingrid Leroy, Phillippe Simková, Hana Valárik, Miroslav Caccamo, Mario Dolezel, Jaroslav Mayer, Klaus F.X. Feuillet, Catherine Tranquilli, Gabriela Paniego, Norma Beatriz Echenique, Carmen Viviana |
| author_browse | Caccamo, Mario Clavijo, Bernardo Dolezel, Jaroslav Echenique, Carmen Viviana Feuillet, Catherine Garbus, Ingrid Gonzalez, Sergio Alberto Helguera, Marcelo Leroy, Phillippe Martis, Mihaela M. Mayer, Klaus F.X. Paniego, Norma Beatriz Rivarola, Maximo Lisandro Simková, Hana Tranquilli, Gabriela Valárik, Miroslav Vanzetti, Leonardo Sebastian |
| author_facet | Helguera, Marcelo Rivarola, Maximo Lisandro Clavijo, Bernardo Martis, Mihaela M. Vanzetti, Leonardo Sebastian Gonzalez, Sergio Alberto Garbus, Ingrid Leroy, Phillippe Simková, Hana Valárik, Miroslav Caccamo, Mario Dolezel, Jaroslav Mayer, Klaus F.X. Feuillet, Catherine Tranquilli, Gabriela Paniego, Norma Beatriz Echenique, Carmen Viviana |
| author_sort | Helguera, Marcelo |
| collection | INTA Digital |
| description | Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223 Mb) and scaffolds (65 Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34 Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the
scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information |
| format | info:ar-repo/semantics/artículo |
| id | INTA1142 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | INTA11422018-10-26T12:40:41Z New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing Helguera, Marcelo Rivarola, Maximo Lisandro Clavijo, Bernardo Martis, Mihaela M. Vanzetti, Leonardo Sebastian Gonzalez, Sergio Alberto Garbus, Ingrid Leroy, Phillippe Simková, Hana Valárik, Miroslav Caccamo, Mario Dolezel, Jaroslav Mayer, Klaus F.X. Feuillet, Catherine Tranquilli, Gabriela Paniego, Norma Beatriz Echenique, Carmen Viviana Trigo Triticum Aestivum Genes Cromosomas Chromosomes Cromosoma 4 D Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223 Mb) and scaffolds (65 Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34 Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; Argentina Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Clavijo, Bernardo. Norwich Research Park. The Genome Analysis Centre; Reino Unido Fil: Martis, Mihaela M.. Helmholtz Zentrum München; Alemania Fil: Vanzetti, Leonardo Sebastián. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuario Marcos Juárez; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Garbus, Ingrid. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur; Argentina Fil: Leroy, Phillippe. Universite Blaise Pascal; Francia. Institut National de la Recherche Agronomique; Francia Fil: Šimková, Hana. Institute of Experimental Botany. Centre of the Region Haná for Biotechnological and Agricultural Research; República Checa Fil: Valárik, Miroslav. Institute of Experimental Botany. Centre of the Region Haná for Biotechnological and Agricultural Research; República Checa Fil: Caccamo, Mario. Norwich Research Park. The Genome Analysis Centre; Reino Unido Fil: Doležel, Jeroslav. Institute of Experimental Botany. Centre of the Region Haná for Biotechnological and Agricultural Research; República Checa Fil: Mayer, Klaus F. X.. Helmholtz Zentrum München; Alemania Fil: Feuillet, Catherine. Bayer Crop Science; Estados Unidos Fil: Tranquilli, Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur; Argentina 2017-09-06T12:48:36Z 2017-09-06T12:48:36Z 2015 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/1142 https://www.sciencedirect.com/science/article/pii/S016894521400291X?via%3Dihub 0168-9452 https://doi.org/10.1016/j.plantsci.2014.12.004 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Plant science 233 : 200-212. (Apr. 2015) |
| spellingShingle | Trigo Triticum Aestivum Genes Cromosomas Chromosomes Cromosoma 4 D Helguera, Marcelo Rivarola, Maximo Lisandro Clavijo, Bernardo Martis, Mihaela M. Vanzetti, Leonardo Sebastian Gonzalez, Sergio Alberto Garbus, Ingrid Leroy, Phillippe Simková, Hana Valárik, Miroslav Caccamo, Mario Dolezel, Jaroslav Mayer, Klaus F.X. Feuillet, Catherine Tranquilli, Gabriela Paniego, Norma Beatriz Echenique, Carmen Viviana New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing |
| title | New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing |
| title_full | New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing |
| title_fullStr | New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing |
| title_full_unstemmed | New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing |
| title_short | New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing |
| title_sort | new insight into the wheat chromosome 4 d structure and virtual gene order relead by survey pyrosequencing |
| topic | Trigo Triticum Aestivum Genes Cromosomas Chromosomes Cromosoma 4 D |
| url | http://hdl.handle.net/20.500.12123/1142 https://www.sciencedirect.com/science/article/pii/S016894521400291X?via%3Dihub https://doi.org/10.1016/j.plantsci.2014.12.004 |
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