Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

Agriculture and Agri Food Canada Morden MB R6M 1Y5 Canada

Arizona Genomics Institute University of Arizona Tucson AZ 85721 USA

Baylor College of Medicine Jan and Dan Duncan Neurological Research Institute Houston TX 77030 USA

Boyce Thompson Institute for Plant Research Cornell University 533 Tower Road Ithaca NY 14853 1801 USA

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

Corn Insects and Crop Genetics Research USDA Agricultural Research Service and Department of Plant Pathology and Microbiology Iowa State University Ames IA 50011 1020 USA

Departamento de Ciencias Basicas Universidad Autonoma Agraria Antonio Narro Narro 1923 Saltillo Coah 25315 México

Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA

Department of Botany and Plant Sciences University of California Riverside CA 92521 USA

Department of Computer Science University of California Riverside CA 92521 USA

Department of Computer Science University of Turin Corso Svizzera 185 10149 Turin Italy

Department of Crop and Soil Environmental Sciences Virginia Tech Blacksburg VA 24061 USA

Department of Crop and Soil Science Oregon State University Corvallis OR 97331 USA

Department of Crop and Soil Sciences Washington State University Pullman WA 99164 USA

Department of Plant and Microbial Biology University of California Berkeley CA 94720 USA

Department of Plant Biology Department of Agronomy and Plant Genetics University of Minnesota St Paul MN 55108 USA

Department of Plant Sciences and Plant Pathology Montana State University Bozeman MT 59717 3150 USA

Department of Plant Sciences University of California Davis CA 95616 USA

Deptartment of Mathematics Statistics and Computer Science Marquette University Milwaukee WI 53233 USA

Dow AgroSciences LLC Indianapolis IN 46268 1054 USA

Google Inc Mountain View CA 94043 USA

Hudson Alpha Genome Sequencing Center DOE Joint Genome Institute Huntsville AL 35806 USA

International Cooperation Department The Scientific and Technological Research Council of Turkey Tunus cad No 80 06100 Kavaklidere Ankara Turkey

Keck School of Medicine University of Southern California Los Angeles CA 90033 USA

Leibniz Institute of Plant Genetics and Crop Plant Research D 06466 Gatersleben Germany

Molefarming Laboratory USA Davis CA 95616 USA

Monsanto Research Center Bangalore 560092 India

Nordic Genetic Resource Center SE 23053 Alnarp Sweden

Ronald Reagan UCLA Medical Center Los Angeles CA 90095 USA

School of Computer Engineering Nanyang Technological University Nanyang Avenue Singapore 639798 Singapore

Swedish University of Agricultural Sciences SE 750 07 Uppsala Sweden

The Sainsbury Laboratory Norwich Research Park Norwich NR4 7UH UK

Turtle Rock Studios Lake Forest CA 92630 USA

US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA

USDA ARS Aberdeen ID 83210 USA

USDA ARS Albany CA 94710 USA

USDA ARS Biosciences Research Lab Fargo ND 58105 USA

USDA University of Missouri Columbia MO 65211 USA

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The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L

A chromosome conformation capture ordered sequence of the barley genome

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