New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing
- Autores
- 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
- Año de publicación
- 2015
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- 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 - Fuente
- Plant science 233 : 200-212. (Apr. 2015)
- Materia
-
Trigo
Triticum Aestivum
Genes
Cromosomas
Chromosomes
Cromosoma 4 D - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- http://creativecommons.org/licenses/by-nc-sa/4.0/
- Repositorio
.jpg)
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/1142
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New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencingHelguera, MarceloRivarola, Maximo LisandroClavijo, BernardoMartis, Mihaela M.Vanzetti, Leonardo SebastianGonzalez, Sergio AlbertoGarbus, IngridLeroy, PhillippeSimková, HanaValárik, MiroslavCaccamo, MarioDolezel, JaroslavMayer, Klaus F.X.Feuillet, CatherineTranquilli, GabrielaPaniego, Norma BeatrizEchenique, Carmen VivianaTrigoTriticum AestivumGenesCromosomasChromosomesCromosoma 4 DSurvey 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 informationFil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; ArgentinaFil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Clavijo, Bernardo. Norwich Research Park. The Genome Analysis Centre; Reino UnidoFil: Martis, Mihaela M.. Helmholtz Zentrum München; AlemaniaFil: Vanzetti, Leonardo Sebastián. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuario Marcos Juárez; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: 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; ArgentinaFil: Leroy, Phillippe. Universite Blaise Pascal; Francia. Institut National de la Recherche Agronomique; FranciaFil: Šimková, Hana. Institute of Experimental Botany. Centre of the Region Haná for Biotechnological and Agricultural Research; República ChecaFil: Valárik, Miroslav. Institute of Experimental Botany. Centre of the Region Haná for Biotechnological and Agricultural Research; República ChecaFil: Caccamo, Mario. Norwich Research Park. The Genome Analysis Centre; Reino UnidoFil: Doležel, Jeroslav. Institute of Experimental Botany. Centre of the Region Haná for Biotechnological and Agricultural Research; República ChecaFil: Mayer, Klaus F. X.. Helmholtz Zentrum München; AlemaniaFil: Feuillet, Catherine. Bayer Crop Science; Estados UnidosFil: Tranquilli, Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: 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; Argentina2017-09-06T12:48:36Z2017-09-06T12:48:36Z2015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/1142https://www.sciencedirect.com/science/article/pii/S016894521400291X?via%3Dihub0168-9452https://doi.org/10.1016/j.plantsci.2014.12.004Plant science 233 : 200-212. (Apr. 2015)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-04T09:46:58Zoai:localhost:20.500.12123/1142instacron: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 09:47:00.315INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse |
| dc.title.none.fl_str_mv |
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 |
| spellingShingle |
New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing Helguera, Marcelo Trigo Triticum Aestivum Genes Cromosomas Chromosomes Cromosoma 4 D |
| title_short |
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_sort |
New insight into the wheat chromosome 4 D structure and virtual gene order, relead by survey pyrosequencing |
| dc.creator.none.fl_str_mv |
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 |
Helguera, Marcelo |
| 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_role |
author |
| author2 |
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 |
| author2_role |
author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Trigo Triticum Aestivum Genes Cromosomas Chromosomes Cromosoma 4 D |
| topic |
Trigo Triticum Aestivum Genes Cromosomas Chromosomes Cromosoma 4 D |
| dc.description.none.fl_txt_mv |
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 |
| 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 |
| publishDate |
2015 |
| dc.date.none.fl_str_mv |
2015 2017-09-06T12:48:36Z 2017-09-06T12:48:36Z |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
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article |
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publishedVersion |
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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 |
| 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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0168-9452 |
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eng |
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eng |
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