TitleThe genome of black raspberry (Rubus occidentalis).
Publication TypeJournal Article
Year of Publication2016
AuthorsVanBuren, R, Bryant, D, Bushakra, JM, Vining, KJ, Edger, PP, Rowley, ER, Priest, HD, Michael, TP, Lyons, E, Filichkin, SA, Dossett, M, Finn, CE, Bassil, NV, Mockler, TC
JournalPlant J
Volume87
Issue6
Pagination535-47
Date Published2016 09
ISSN1365-313X
KeywordsCentromere, Chromosome Mapping, Disease Resistance, Fruit, Gene Duplication, Gene Expression Regulation, Plant, Genome, Plant, Genomics, Plant Diseases, Rosaceae, Rubus, Sequence Analysis, DNA, Verticillium
Abstract

Black 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.

DOI10.1111/tpj.13215
Alternate JournalPlant J.
PubMed ID27228578