A chromosome conformation capture ordered sequence of the barley genome

By M. Mascher, H. Gundlach, A. Himmelbach, Sebastian Beier, Sven Twardziok, T. Wicker, V. Radchuk, C. Dockter, P. Hedley, J. Russell and 66 more. Nature, 2017

1,250 citations recorded by the source corpus.

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, highlighting regions vulnerable to genetic erosion. The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare. Triticeae grasses, which include barley, wheat and rye, are widely cultivated plants with particularly complex genomes and evolutionary histories. Sequencing of the barley genome has been particularly challenging owing to its large size and particular genomic features, such as an abundance of repetitive elements. Nils Stein and colleagues of the International Barley Genome Sequencing Consortium report sequencing and assembly of a reference genome for barley (Hordeumvulgare L). They use a combined approach of hierarchical shotgun sequencing of bacterial artificial chromosomes, genome mapping on nanochannel arrays and chromosome-scale scaffolding with Hi-C sequencing. This brings the first comprehensive, completely ordered assembly of the pericentromeric regions of a Triticeae genome. The authors also sequenced and examined genetic diversity in the exomes of 96 European elite barley lines with a spring or winter growth habit, and highlight the utility of this resource for cereal genomics and breeding programs.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/204397690b00cd9652ced1ecc80d63585bb167b6

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Citations in the corpus

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species (2017, background): “For example, the latest assembly of the barley genome (18) has been added to the resource and comprises just 6,347 scaffolds with an N50 of 1.9 Mb (cf. the previous assembly, which contained 376 261 unscaffolded contigs of over 1 Kb in length with an N50 of just 1.4 Kb).”
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 (2018, methodology): “Hi-C, a method for determining the 3D configuration of chromatin, is emerging as a valuable source of data for genome assembly (Lieberman-Aiden et al. 2009; Burton et al. 2013; Session et al. 2016; Peichel et al. 2016; Bickhart et al. 2017; Dudchenko et al. 2017; Mascher et al. 2017).”
Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model (2020, neutral): “In plants and animals, for example, genes with roles in immunity often cluster and are located in dynamic regions (Gokcumen et al. , 2011; Kawakatsu et al. , 2016; Laun et al. , 2006; Leister, 2004; Mascher et al. , 2017; Roach et al. , 2005; Seidl and Thomma, 2017).”
Improving Flooding Tolerance of Crop Plants (2018, background): “Zea mays yes yes (Table 2) [45,46] available Triticum aestivum yes yes [47] not available Hordeum vulgare yes yes (Table 3) [48] not available Avena sativa unknown no not available not available Secale cereale unknown no [49] not available Lolium perenne yes yes [50] not available”
Multiple wheat genomes reveal global variation in modern breeding (2020, methodology): “6b, Supplementary Tables 17, 18).”