Authors: Mascher, Martin and Gundlach, Heidrun and Himmelbach, Axel and Beier, Sebastian and Twardziok, Sven O and Wicker, Thomas and Radchuk, Volodymyr and Dockter, Christoph and Hedley, Pete E and Russell, Joanne and Bayer, Micha and Ramsay, Luke and Liu, Hui and Haberer, Georg and Zhang, Xiao-Qi and Zhang, Qisen and Barrero, Roberto A and Li, Lin and Taudien, Stefan and Groth, Marco and Felder, Marius and Hastie, Alex and Šimková, Hana and Stanková, Helena and Vrána, Jan and Chan, Saki and Muñoz-Amatriaín, María and Ounit, Rachid and Wanamaker, Steve and Bolser, Daniel and Colmsee, Christian and Schmutzer, Thomas and Aliyeva-Schnorr, Lala and Grasso, Stefano and Tanskanen, Jaakko and Chailyan, Anna and Sampath, Dharanya and Heavens, Darren and Clissold, Leah and Cao, Sujie and Chapman, Brett and Dai, Fei and Han, Yong and Li, Hua and Li, Xuan and Lin, Chongyun and McCooke, John K and Tan, Cong and Wang, Penghao and Wang, Songbo and Yin, Shuya and Zhou, Gaofeng and Poland, Jesse A and Bellgard, Matthew I and Borisjuk, Ljudmilla and Houben, Andreas and Doležel, Jaroslav and Ayling, Sarah and Lonardi, Stefano and Kersey, Paul and Langridge, Peter and Muehlbauer, Gary J and Clark, Matthew D and Caccamo, Mario and Schulman, Alan H and Mayer, Klaus F X and Platzer, Matthias and Close, Timothy J and Scholz, Uwe and Hansson, Mats and Zhang, Guoping and Braumann, Ilka and Spannagl, Manuel and Li, Chengdao and Waugh, Robbie and Stein, Nils
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.