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.

Bayer Crop Science 3500 Paramount Parkway Morrisville NC 27560 USA

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany Sokolovska 6 CZ 77200 Olomouc Czech Republic

CERZOS and Universidad Nacional del Sur Bahía Blanca Buenos Aires Argentina

Estación Experimental Agropecuaria Marcos Juárez Instituto Nacional de Tecnología Agropecuaria Argentina

Estación Experimental Agropecuaria Marcos Juárez Instituto Nacional de Tecnología Agropecuaria Marcos Juárez Córdoba Argentina

INRA UMR 1095 Genetics Diversity and Ecophysiology of Cereals Institut National de la Recherche Agronomique Université Blaise Pascal Clermont Ferrand France

Instituto de Biotecnología Centro Investigación en Ciencias Veterinarias y Agronómicas Argentina

Instituto de Recursos Biológicos CIRN INTA Hurlingham Buenos Aires Argentina

MIPS IBIS Helmholtz Zentrum München 85764 Neuherberg Germany

The Genome Analysis Centre Norwich Research Park Norwich NR4 7UH UK

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The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order

Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes

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