A chromosome conformation capture ordered sequence of the barley genome

Abstract

Barley remains dated to the dawn of agriculture have been found at several archaeological sites 1,2 . In addition to indications that barley was an important food crop, recent excavations have fuelled speculation that beverages from fermented grains may have motivated early Neolithic hunter-gatherers to erect some of humankind's oldest monuments 3,4 . Moreover, brewing beer may also have played a role in the eastward spread of the crop after its initial domestication in the Fertile Crescent 5,6 . Since 2012, both genetic research and crop improvement in barley have benefited from a partly ordered draft sequence assembly 7 . This community resource has underpinned gene isolation 8,9 and population genomic studies 10 . However, these and other efforts have also revealed limitations of the current draft assembly. The limitations are often direct consequences of two characteristic genomic features: the extreme abundance of repetitive elements, and the severely reduced frequency of meiotic recombination in pericentromeric regions 11 .These factors have limited the contiguity of whole-genome assemblies to kilobase-sized sequences originating from low-copy regions of the genome. Thus, a detailed investigation of the composition of the repetitive fraction of the genome-including expanded gene families-and of the distribution of targets of selection and crop improvement in (genetically defined) pericentromeric regions has been beyond reach.Here we present a map-based reference sequence of the barley genome including the first comprehensively ordered assembly of the pericentromeric regions of a Triticeae genome. The resource highlights a conspicuous distinction between distal and proximal regions of chromosomes that is reflected by the intranuclear chromatin organization. Moreover, chromosomal compartments are differentiated by an exponential gradient of gene density and recombination rate, striking contrasts in the distribution of retrotransposon families, and distinct patterns of genetic diversity.Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlightin...

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

“…For example, hybrid scaffolding was used to enhance the genome assemblies of amaranth (Amaranthus hypochondriacus; Clouse et al, 2016), barley (Hordeum vulgare; Mascher et al, 2017), and quinoa (Chenopodium quinoa; Jarvis et al, 2017). In amaranth, the hybrid assembly reduced the number of scaffolds from 343 to 241 and nearly doubled the final scaffold N50 by making several key connections between existing large scaffolds.…”

“…Hi-C is a relatively new approach that is gaining rapid acceptance because of the resulting useful arrangements of contigs in chromosome-scale scaffolds (Korbel and Lee, 2013;Bickhart et al, 2017;Dudchenko et al, 2017;Mascher et al, 2017). Hi-C was originally developed to detect intra-and interchromosomal interactions such as those between enhancers and promoter regions, but it has proven to be useful for long-range scaffolding of sequence contigs as well.…”

Map-based cloning of the fertility restoration locus Rfm1 in cultivated barley (Hordeum vulgare)

“…Recently, the International Barley Genome Sequencing Consortium (IBGS) published a highquality reference genome sequence of the elite cultivar Morex (Mascher et al 2017). Approximately 84% of the genome is composed of mobile elements or other repeated sequences (Mayer et al 2012;Mascher et al 2017). The majority of these consists of retrotransposons, 99.6% of which are long terminal repeat (LTR) retrotransposons.…”

“…Because of its diploid genome, barley is considered a model crop for the Triticeae tribe, which includes wheat (Triticum aestivum). Recently, the International Barley Genome Sequencing Consortium (IBGS) published a highquality reference genome sequence of the elite cultivar Morex (Mascher et al 2017). Approximately 84% of the genome is composed of mobile elements or other repeated sequences (Mayer et al 2012;Mascher et al 2017).…”

From genes to networks

“…The sequencing and assembly of high-quality 'platinum' genomes [6][7][8] further empowers plant scientists to pursue the details of genetic regulation and deepen our understanding of plant evolution. For example, in this issue, Wan and colleagues 9 report a high-quality draft genome of Gnetum montanum, a gymnosperm and the first sequenced species for gnetophytes.…”