Structural and functional partitioning of bread wheat chromosome 3B.

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Abstract

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.

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The Sorghum bicolor genome and the diversification of grasses.

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Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

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Author and article information

Journal

Journal ID (iso-abbrev): Science

Title: Science (New York, N.Y.)

ISSN (Electronic): 1095-9203

ISSN (Print): 0036-8075

Publication date (Electronic): Jul 18 2014

Volume: 345

Issue: 6194

Affiliations

[1 ] Institut National de la Recherche Agronomique (INRA) 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. frederic.choulet@clermont.inra.fr.

[2 ] 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.

[3 ] Institut National de la Recherche Agronomique (INRA) 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.

[4 ] INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France.

[5 ] Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France.

[6 ] Biométrie et Intelligence Artificielle, INRA, Chemin de Borde Rouge, BP 27, 31326 Castanet-Tolosan, France.

[7 ] Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic.

[8 ] The Genome Analysis Centre, Norwich, Norwich Research Park, Norwich NR4 7UH, UK.

[9 ] Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052 Gent, Belgium.

[10 ] Munich Information Center for Protein Sequences, Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany.

[11 ] 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.

Article

Publisher Item ID: 345/6194/1249721

DOI: 10.1126/science.1249721

PubMed ID: 25035497

SO-VID: f504066b-64b9-45a3-a322-326bbe12b3eb

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