These authors contributed equally to this work. SUMMARYBlack raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein-coding genes, we identified 290 very recent small-scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

European hazelnut (Corylus avellana L.) is of global agricultural and economic significance, with genetic diversity existing in hundreds of accessions. Breeding efforts have focused on maximizing nut yield and quality and reducing susceptibility to diseases such as Eastern filbert blight (EFB). Here we present the first sequenced genome among the order Fagales, the EFB-resistant diploid hazelnut accession 'Jefferson' (OSU 703.007). We assembled the highly heterozygous hazelnut genome using an Illumina only approach and the final assembly has a scaffold N50 of 21.5kb. We captured approximately 91 percent (345 Mb) of the flow-cytometry-determined genome size and identified 34,910 putative gene loci. In addition, we identified over 2 million polymorphisms across seven diverse hazelnut accessions and characterized t heir effect on coding sequences. We produced t wo high-density genetic maps with 3,209 markers from an F1 hazelnut population, representing a five-fold increase in marker density over previous maps. These genomic resources will aide in the discovery of molecular markers linked to genes of interest for hazelnut breeding efforts, and are available to the community at https://www.cavellanagenomeportal.com/.