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Title: The genome of black raspberry (Rubus occidentalis)

item VANBUREN, ROBERT - Danforth Plant Science Center
item BRYANT, DOUGLAS - Newleaf Symbiotics
item Bushakra, Jill
item VINING, KELLY - Oregon State University
item EDGER, PATRICK - Danforth Plant Science Center
item ROWLEY, ERIK - Danforth Plant Science Center
item PRIEST, HENRY - Danforth Plant Science Center
item MICHAEL, TODD - Ibis Biosciences
item LYONS, ERIC - University Of Arizona
item FILICHKIN, SERGEI - Oregon State University
item DOSSETT, MICHAEL - Pacific Agri-Food Research Center
item Finn, Chad
item Bassil, Nahla
item MOCKLER, TODD - Danforth Plant Science Center

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2016
Publication Date: 7/20/2016
Citation: Vanburen, R., Bryant, D.W., Bushakra, J., Vining, K.J., Edger, P.P., Rowley, E.R., Priest, H.D., Michael, T.P., Lyons, E., Filichkin, S.A., Dossett, M., Finn, C.E., Bassil, N.V., Mockler, T.C. 2016. The genome of black raspberry (Rubus occidentalis). Plant Journal. 87(6):535-547. doi: 10.1111/tpj.13215.

Interpretive Summary: Black raspberry is an important specialty crop in the US Pacific Northwest. We have sequenced the nuclear and chloroplast genomes of a black raspberry selected for it's low genetic diversity and resistance to the fungal pathogen verticillium wilt. We have compared the black raspberry genome sequence with the genomes of strawberry and peach and have found associations among the three crops. This information will be valuable for breeders of crops in the Rose Family.

Technical Abstract: Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the U.S. 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.