title: The genome of black raspberry (Rubus occidentalis).
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.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
authors.forename: Doug
authors.initials: D
authors.lastname: Bryant
authors.affiliation: USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA.
authors.forename: Jill M
authors.initials: JM
authors.lastname: Bushakra
authors.affiliation: Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA.|Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA.
authors.forename: Kelly J
authors.initials: KJ
authors.lastname: Vining
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
authors.forename: Erik R
authors.initials: ER
authors.lastname: Rowley
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
authors.forename: Henry D
authors.initials: HD
authors.lastname: Priest
authors.affiliation: Ibis Biosciences, Carlsbad, CA, USA.
authors.forename: Todd P
authors.initials: TP
authors.lastname: Michael
authors.affiliation: CyVerse, BIO5, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.affiliation: Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA.|Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University Corvallis, Corvallis, OR, 97331, USA.
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Filichkin
authors.affiliation: B.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) - Agassiz Research and Development Centre, Agassiz, BC, VOM 1A0, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Dossett
authors.affiliation: USDA-ARS Horticultural Crops Research Unit, Corvallis, OR, 97330, USA.
authors.forename: Chad E
authors.initials: CE
authors.lastname: Finn
authors.affiliation: USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA.
authors.forename: Nahla V
authors.initials: NV
authors.lastname: Bassil
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA. tmockler@danforthcenter.org.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
mesh_terms: D002503:Centromere / Q000235:genetics; D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics; D005638:Fruit / Q000235:genetics / Q000502:physiology; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D027824:Rosaceae / Q000235:genetics; D065856:Rubus / Q000235:genetics* / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D020172:Verticillium / Q000472:pathogenicity
keywords: black raspberry; genome assembly; improvement; neofunctionalization; tandem gene duplicates