title: New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing.
abstract: 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.
authors.affiliation: Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina. Electronic address: helguera.marcelo@inta.gob.ar.
authors.forename: Marcelo
authors.initials: M
authors.lastname: Helguera
authors.affiliation: 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.
authors.forename: Máximo
authors.initials: M
authors.lastname: Rivarola
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK. Electronic address: bernardo.clavijo@tgac.ac.uk.
authors.forename: Bernardo
authors.initials: B
authors.lastname: Clavijo
authors.affiliation: MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany. Electronic address: mihaela.martis@helmholtz-muenchen.de.
authors.forename: Mihaela M
authors.initials: MM
authors.lastname: Martis
authors.affiliation: 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.
authors.forename: Leonardo S
authors.initials: LS
authors.lastname: Vanzetti
authors.affiliation: 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.
authors.forename: Sergio
authors.initials: S
authors.lastname: González
authors.affiliation: 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.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Garbus
authors.affiliation: 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.
authors.forename: Phillippe
authors.initials: P
authors.lastname: Leroy
authors.affiliation: 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.
authors.forename: Hana
authors.initials: H
authors.lastname: Šimková
authors.affiliation: 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.
authors.forename: Miroslav
authors.initials: M
authors.lastname: Valárik
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK. Electronic address: mario.caccamo@tgac.ac.uk.
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.affiliation: 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.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany. Electronic address: k.mayer@helmholtz-muenchen.de.
authors.forename: Klaus F X
authors.initials: KFX
authors.lastname: Mayer
authors.affiliation: Bayer Crop Science, 3500 Paramount Parkway Morrisville, NC 27560, USA. Electronic address: catherine.feuillet@bayer.com.
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
authors.affiliation: Instituto de Recursos Biológicos, CIRN, INTA, Hurlingham, Buenos Aires, Argentina. Electronic address: tranquilli.gabriela@inta.gob.ar.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Tranquilli
authors.affiliation: 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.
authors.forename: Norma
authors.initials: N
authors.lastname: Paniego
authors.affiliation: 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.
authors.forename: Viviana
authors.initials: V
authors.lastname: Echenique
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D020224:Expressed Sequence Tags / Q000737:chemistry; D023061:Gene Order; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics*
keywords: Chromosome 4D survey sequence; Gene annotation; Gene content; Synteny; Triticum aestivum; Virtual gene order