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 replicative spread of retrotransposons in the genome creates new insertional polymorphisms, increasing retrotransposon numbers and potentially both their share of the genome and genome size. The BARE -1 retrotransposon constitutes a major, dispersed, active component of Hordeum genomes, and BARE -1 number is positively correlated with genome size. We have examined genome size and BARE -1 insertion patterns and number in wild barley, Hordeum spontaneum , in Evolution Canyon, Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. BARE -1 has been sufficiently active for its insertional pattern to resolve individuals in a way consonant with their ecogeographical distribution in the canyon and to distinguish them from provenances outside the canyon. On both slopes, but especially on the drier south-facing slope, a simultaneous increase in the BARE -1 copy number and a decrease in the relative number lost through recombination, as measured by the abundance of solo long terminal repeats, appear to have driven the BARE -1 share of the genome upward with the height and dryness of the slope. The lower recombinational loss would favor maintenance of more full-length copies, enhancing the ability of the BARE -1 family to contribute to genome size growth. These local data are consistent with regional trends for BARE -1 in H. spontaneum across Israel and therefore may reflect adaptive selection for increasing genome size through retrotransposon activity.

Yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease threatening much of global wheat production. Race-specific resistance (R)-genes are used to control rust diseases, but the rapid emergence of virulent Pst races has prompted the search for a more durable resistance. Here, we report the cloning of Yr15, a broad-spectrum R-gene derived from wild emmer wheat, which encodes a putative kinase-pseudokinase protein, designated as wheat tandem kinase 1, comprising a unique R-gene structure in wheat. The existence of a similar gene architecture in 92 putative proteins across the plant kingdom, including the barley RPG1 and a candidate for Ug8, suggests that they are members of a distinct family of plant proteins, termed here tandem kinase-pseudokinases (TKPs). The presence of kinase-pseudokinase structure in both plant TKPs and the animal Janus kinases sheds light on the molecular evolution of immune responses across these two kingdoms.