New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Autores
Helguera, Marcelo; Rivarola, Maximo Lisandro; Clavijo, Bernardo; Martis, Mihaela M.; Vanzetti, Leonardo Sebastián; Gonzalez, Sergio Alberto; Garbus, Ingrid; Leroy, Phillippe; Šimková, Hana; Valárik, Miroslav; Caccamo, Mario; Doležel, Jeroslav; Mayer, Klaus F. X.; Feuillet, Catherine; Tranquilli, Gabriela; Paniego, Norma Beatriz; Echenique, 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. Centro Regional Córdoba. Estación Experimental Agropecuario Marcos Juarez; Argentina
Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. 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. Centro Regional Córdoba. Estación Experimental Agropecuario Marcos Juarez; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. 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(i); 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. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Echenique, Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida(i); Argentina. Universidad Nacional del Sur; Argentina
Materia
Chromosome 4d Survey Sequence
Gene Annotation
Gene Content
Synteny
Virtual Gene Order
Triticum Aestivum
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/11772
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/11772
network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencingHelguera, MarceloRivarola, Maximo LisandroClavijo, BernardoMartis, Mihaela M.Vanzetti, Leonardo SebastiánGonzalez, Sergio AlbertoGarbus, IngridLeroy, PhillippeŠimková, HanaValárik, MiroslavCaccamo, MarioDoležel, JeroslavMayer, Klaus F. X.Feuillet, CatherineTranquilli, GabrielaPaniego, Norma BeatrizEchenique, VivianaChromosome 4d Survey SequenceGene AnnotationGene ContentSyntenyVirtual Gene OrderTriticum Aestivumhttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4Survey 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. Centro Regional Córdoba. Estación Experimental Agropecuario Marcos Juarez; ArgentinaFil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. 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. Centro Regional Córdoba. Estación Experimental Agropecuario Marcos Juarez; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. 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(i); 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. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; ArgentinaFil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Echenique, Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida(i); Argentina. Universidad Nacional del Sur; ArgentinaElsevier Ireland2015-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/11772Helguera, Marcelo; Rivarola, Maximo Lisandro; Clavijo, Bernardo; Martis, Mihaela M.; Vanzetti, Leonardo Sebastián; et al.; New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing; Elsevier Ireland; Plant Science; 233; 4-2015; 200-20120168-9452enginfo:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S016894521400291Xinfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.plantsci.2014.12.004info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:14:23Zoai:ri.conicet.gov.ar:11336/11772instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-10 13:14:23.777CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
title New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
spellingShingle New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
Helguera, Marcelo
Chromosome 4d Survey Sequence
Gene Annotation
Gene Content
Synteny
Virtual Gene Order
Triticum Aestivum
title_short New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
title_full New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
title_fullStr New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
title_full_unstemmed New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
title_sort New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
dc.creator.none.fl_str_mv Helguera, Marcelo
Rivarola, Maximo Lisandro
Clavijo, Bernardo
Martis, Mihaela M.
Vanzetti, Leonardo Sebastián
Gonzalez, Sergio Alberto
Garbus, Ingrid
Leroy, Phillippe
Šimková, Hana
Valárik, Miroslav
Caccamo, Mario
Doležel, Jeroslav
Mayer, Klaus F. X.
Feuillet, Catherine
Tranquilli, Gabriela
Paniego, Norma Beatriz
Echenique, Viviana
author Helguera, Marcelo
author_facet Helguera, Marcelo
Rivarola, Maximo Lisandro
Clavijo, Bernardo
Martis, Mihaela M.
Vanzetti, Leonardo Sebastián
Gonzalez, Sergio Alberto
Garbus, Ingrid
Leroy, Phillippe
Šimková, Hana
Valárik, Miroslav
Caccamo, Mario
Doležel, Jeroslav
Mayer, Klaus F. X.
Feuillet, Catherine
Tranquilli, Gabriela
Paniego, Norma Beatriz
Echenique, Viviana
author_role author
author2 Rivarola, Maximo Lisandro
Clavijo, Bernardo
Martis, Mihaela M.
Vanzetti, Leonardo Sebastián
Gonzalez, Sergio Alberto
Garbus, Ingrid
Leroy, Phillippe
Šimková, Hana
Valárik, Miroslav
Caccamo, Mario
Doležel, Jeroslav
Mayer, Klaus F. X.
Feuillet, Catherine
Tranquilli, Gabriela
Paniego, Norma Beatriz
Echenique, 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 Chromosome 4d Survey Sequence
Gene Annotation
Gene Content
Synteny
Virtual Gene Order
Triticum Aestivum
topic Chromosome 4d Survey Sequence
Gene Annotation
Gene Content
Synteny
Virtual Gene Order
Triticum Aestivum
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
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. Centro Regional Córdoba. Estación Experimental Agropecuario Marcos Juarez; Argentina
Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. 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. Centro Regional Córdoba. Estación Experimental Agropecuario Marcos Juarez; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. 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(i); 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. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro Nacional de Investigaciones Agropecuarias. Centro de Investigación de Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Echenique, Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida(i); 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 2015-04
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/11336/11772
Helguera, Marcelo; Rivarola, Maximo Lisandro; Clavijo, Bernardo; Martis, Mihaela M.; Vanzetti, Leonardo Sebastián; et al.; New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing; Elsevier Ireland; Plant Science; 233; 4-2015; 200-2012
0168-9452
url http://hdl.handle.net/11336/11772
identifier_str_mv Helguera, Marcelo; Rivarola, Maximo Lisandro; Clavijo, Bernardo; Martis, Mihaela M.; Vanzetti, Leonardo Sebastián; et al.; New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing; Elsevier Ireland; Plant Science; 233; 4-2015; 200-2012
0168-9452
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S016894521400291X
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.plantsci.2014.12.004
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier Ireland
publisher.none.fl_str_mv Elsevier Ireland
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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