We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.

Biométrie et Intelligence Artificielle INRA Chemin de Borde Rouge BP 27 31326 Castanet Tolosan France

Centre National des Ressources Génomiques Végétales INRA UPR 1258 24 Chemin de Borde Rouge 31326 Castanet Tolosan France

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany Slechtitelu 31 CZ 78371 Olomouc Czech Republic

Commissariat à l'Energie Atomique et aux Energies Alternatives Direction des Sciences du Vivant Institut de Génomique Genoscope 2 Rue Gaston Crémieux 91000 Evry France

Commissariat à l'Energie Atomique et aux Energies Alternatives Direction des Sciences du Vivant Institut de Génomique Genoscope 2 Rue Gaston Crémieux 91000 Evry France CNRS UMR 8030 2 Rue Gaston Crémieux 91000 Evry France Université d'Evry CP5706 Evry France

Department of Plant Systems Biology Technologiepark 927 9052 Gent Belgium

INRA UR1164 Unité de Recherche Génomique Info Research Unit in Genomics Info INRA de Versailles Route de Saint Cyr 78026 Versailles France

Institut National de la Recherche Agronomique UMR1095 Genetics Diversity and Ecophysiology of Cereals 5 Chemin de Beaulieu 63039 Clermont Ferrand France University Blaise Pascal UMR1095 Genetics Diversity and Ecophysiology of Cereals 5 Chemin de Beaulieu 63039 Clermont Ferrand France

Munich Information Center for Protein Sequences Institute of Bioinformatics and Systems Biology Helmholtz Zentrum Muenchen D 85764 Neuherberg Germany

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

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