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

Autor: Helguera M; Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina. Electronic address: helguera.marcelo@inta.gob.ar., Rivarola M; Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. Electronic address: rivarola.maximo@inta.gob.ar., Clavijo B; The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK. Electronic address: bernardo.clavijo@tgac.ac.uk., Martis MM; MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany. Electronic address: mihaela.martis@helmholtz-muenchen.de., Vanzetti LS; Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. Electronic address: vanzetti.leonardo@inta.gob.ar., González S; Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. Electronic address: gonzalez.sergio@inta.gob.ar., Garbus I; CERZOS (Centro de Recursos Naturales Renovables de la Zona Semiárida), (CCT-CONICET-Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Buenos Aires, Argentina. Electronic address: igarbus@criba.edu.ar., Leroy P; INRA-UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche Agronomique-Université Blaise Pascal, Clermont-Ferrand, France. Electronic address: philippe.leroy@clermont.inra.fr., Šimková H; Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic. Electronic address: SimkovaH@ueb.cas.cz., Valárik M; Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic. Electronic address: valarik@ueb.cas.cz., Caccamo M; The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK. Electronic address: mario.caccamo@tgac.ac.uk., Doležel J; Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic. Electronic address: dolezel@ueb.cas.cz., Mayer KFX; MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany. Electronic address: k.mayer@helmholtz-muenchen.de., Feuillet C; Bayer Crop Science, 3500 Paramount Parkway Morrisville, NC 27560, USA. Electronic address: catherine.feuillet@bayer.com., Tranquilli G; Instituto de Recursos Biológicos, CIRN, INTA, Hurlingham, Buenos Aires, Argentina. Electronic address: tranquilli.gabriela@inta.gob.ar., Paniego N; Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. Electronic address: paniego.norma@inta.gob.ar., Echenique V; CERZOS (Centro de Recursos Naturales Renovables de la Zona Semiárida), (CCT-CONICET-Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Buenos Aires, Argentina. Electronic address: echeniq@criba.edu.ar.
Jazyk: angličtina
Zdroj: Plant science : an international journal of experimental plant biology [Plant Sci] 2015 Apr; Vol. 233, pp. 200-212. Date of Electronic Publication: 2014 Dec 18.
DOI: 10.1016/j.plantsci.2014.12.004
Abstrakt: 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 (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb 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.
(Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.)
Databáze: MEDLINE
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