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

Authors
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
Publication Year
2015
Language
English
Format
article
Status
Published version
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
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
Source
Plant science 233 : 200-212. (Apr. 2015)
Subject
Trigo
Triticum Aestivum
Genes
Cromosomas
Chromosomes
Cromosoma 4 D
Access level
Open access
License
Repository
INTA Digital (INTA)
Institution
Instituto Nacional de Tecnología Agropecuaria
OAI Identifier
oai:localhost:20.500.12123/1142