The genome of black raspberry (Rubus occidentalis)

Robert VanBuren, Doug Bryant, Jill M. Bushakra, Kelly J. Vining, Patrick P. Edger, Erik R. Rowley, Henry D. Priest, Todd P. Michael, Eric H Lyons, Sergei A. Filichkin, Michael Dossett, Chad E. Finn, Nahla V. Bassil, Todd C. Mockler

Research output: Contribution to journalArticle

37 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)535-547
Number of pages13
JournalPlant Journal
Volume87
Issue number6
DOIs
StatePublished - Sep 1 2016

Fingerprint

Rubus occidentalis
Genome
genome
Fragaria vesca
Rubus idaeus
blackberries
Rubus
Fruit
fruit crops
Fragaria
domestication
fruiting
fruit diseases
specialty crops
duplicate genes
Verticillium dahliae
raspberries
centromeres
Rosaceae
gene duplication

Keywords

  • black raspberry
  • genome assembly
  • improvement
  • neofunctionalization
  • tandem gene duplicates

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology

Cite this

VanBuren, R., Bryant, D., Bushakra, J. M., Vining, K. J., Edger, P. P., Rowley, E. R., ... Mockler, T. C. (2016). The genome of black raspberry (Rubus occidentalis). Plant Journal, 87(6), 535-547. https://doi.org/10.1111/tpj.13215

The genome of black raspberry (Rubus occidentalis). / VanBuren, Robert; Bryant, Doug; Bushakra, Jill M.; Vining, Kelly J.; Edger, Patrick P.; Rowley, Erik R.; Priest, Henry D.; Michael, Todd P.; Lyons, Eric H; Filichkin, Sergei A.; Dossett, Michael; Finn, Chad E.; Bassil, Nahla V.; Mockler, Todd C.

In: Plant Journal, Vol. 87, No. 6, 01.09.2016, p. 535-547.

Research output: Contribution to journalArticle

VanBuren, R, Bryant, D, Bushakra, JM, Vining, KJ, Edger, PP, Rowley, ER, Priest, HD, Michael, TP, Lyons, EH, Filichkin, SA, Dossett, M, Finn, CE, Bassil, NV & Mockler, TC 2016, 'The genome of black raspberry (Rubus occidentalis)', Plant Journal, vol. 87, no. 6, pp. 535-547. https://doi.org/10.1111/tpj.13215
VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER et al. The genome of black raspberry (Rubus occidentalis). Plant Journal. 2016 Sep 1;87(6):535-547. https://doi.org/10.1111/tpj.13215
VanBuren, Robert ; Bryant, Doug ; Bushakra, Jill M. ; Vining, Kelly J. ; Edger, Patrick P. ; Rowley, Erik R. ; Priest, Henry D. ; Michael, Todd P. ; Lyons, Eric H ; Filichkin, Sergei A. ; Dossett, Michael ; Finn, Chad E. ; Bassil, Nahla V. ; Mockler, Todd C. / The genome of black raspberry (Rubus occidentalis). In: Plant Journal. 2016 ; Vol. 87, No. 6. pp. 535-547.
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