In barley, stretches of genomic sequence as large as several hundred kilobases may be entirely composed of nested transposable elements ( Wicker et al., 2005). Using these analytical approaches and libraries with various insert sizes, whole-genome shotgun assemblies of the bread wheat ( Triticum aestivum) progenitors Triticum urartu ( Ling et al., 2013) and Aegilops tauschii ( Jia et al., 2013) have been published recently.Ī major challenge in applying whole-genome shotgun sequencing to large and complex plant genomes is their highly repetitive structure. In addition, the development of innovative sequence assembly algorithms made it possible to obtain robust whole-genome shotgun assemblies of mammalian genomes using only paired-end NGS sequencing reads of different insert sizes ( Gnerre et al., 2011). After a combination of sequencing of a small number of bacterial artificial chromosomes ( BACs Wicker et al., 2006 Steuernagel et al., 2009 Taudien et al., 2011) and shallow whole-genome sequencing ( Wicker et al., 2008) demonstrated the utility of NGS for assembling a large and complex genome, the prospects of obtaining a high-utility sequence of the barley genome were considerably enhanced. The extent to which genomic research in a crop species may be spurred by the availability of a reference genome is aptly illustrated by the large number of agronomically important rice ( Oryza sativa) genes that have been successfully cloned since the release of the rice genome sequence (for review, see Huang et al., 2013).īefore the advent of next-generation sequencing ( NGS) technology, the scale of a barley genome project seemed daunting, owing to the large size (5.1 Gb) and the high repeat content.
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However, the full exploitation of these resources for basic research and crop improvement has been hampered by the lack of a reference genome sequence. Moreover, comprehensive germplasm collections from cultivars and wild accessions ( van Hintum and Menting, 2003) as well as extensive mutant collections ( Druka et al., 2011) provide a sound foundation for genetic studies into developmental and morphological processes. A wealth of genomic resources such as dense genetic maps, ESTs, complementary DNA libraries, and an atlas of gene expression have been developed in the past two decades (for review, see Schulte et al., 2009). It is among the earliest domesticated crop plants and is adapted to a wide range of environmental conditions. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.īarley ( Hordeum vulgare) is an important source of human and animal nutrition and underpins the malting and brewing industries. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. Barley ( Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics.