Sequence and Analysis of the Black Raspberry (Rubus occidentalis) Genome

The US Pacific Northwest is the primary production region of black raspberry, and this high-value specialty crop has been underutilized for several decades. Black raspberries contain high levels of anthocyanins and other bioactive compounds, which has sparked a renewed interest in breeding programs and cultivation. Despite this potential, black raspberry stands have seen a marked decline that many attribute to disease pressures and only three new cultivars have been released over the last 20 years. Here we discuss the available genomic resources for black raspberry, including the recently released draft genome. These resources will expedite marker-assisted improvement of raspberry with applications across the Rosaceae family. The 243 Mb black raspberry genome was sequenced using an Illumina-based whole genome shotgun sequencing approach, and a chromosome-scale assembly was generated using a high-density genetic map. Black raspberry is the sixth genome to be sequenced in the Rosaceae facilitating in-depth comparative genomics across the family. Black raspberry and the diploid wild strawberry (Fragaria vesca) are largely collinear with some lineage-specific structural rearrangements. The genome has 28,005 genes which is comparable to other Rosaceae species and includes a number of recently duplicated genes which may be related to domestication. Gene expression atlases during fruit ripening and Verticillium inoculation provide insights into ripening and disease resistance, respectively. Together the resources discussed here will provide tools for the improved understanding and breeding of Rosaceae crops.