title: Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.
abstract: 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.
authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
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authors.affiliation: Department of Computer Science, University of California, Riverside, CA, 92521, USA.
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authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
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authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.|The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
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authors.affiliation: Department of Computer Science, University of California, Riverside, CA, 92521, USA.
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mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D001467:Hordeum / Q000235:genetics*; D008969:Molecular Sequence Data
keywords: Aegilops tauschii; BAC sequencing; Barley; HarvEST:Barley; Hordeum vulgare L.; centromere BACs; gene distribution; recombination frequency; synteny