The genome of black raspberry (Rubus occidentalis)

Abstract

These authors contributed equally to this work. SUMMARYBlack 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.

Target Capture Sequencing Unravels Rubus Evolution

“…We used the Rubus occidentalis genome v1 assembly (VanBuren et al, 2016) and a conserved set of loci from Fragaria vesca, Malus × domestica and Prunus persica (Liston, 2014). Exon sequences were extracted from the R. occidentalis transcriptome assembly (VanBuren et al, 2016).…”

“…Reads for each sample were mapped to the R. occidentalis chloroplast reference genome (VanBuren et al, 2016) edited with BBMap to contain only one copy of the inverted repeat (Bushnell, 2014;VanBuren et al, 2016). Consensus chloroplast sequences from a reduced read set of up to 100,000 mapped reads were extracted using Geneious v. 9.1.7 with Ns inserted at sites with no sequence coverage (Kearse et al, 2012).…”

Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

“…A comparative genomic approach (Bosi et al, 2015;189 Pop et al, 2004) was used as part of the genome assembly. Specifically, the most recently 190 assembled genomes of closely related species Potentilla micranthia (Buti et al, 2018), Rubus 191 occidentalis (VanBuren et al, 2016), and Fragaria vesca (Edger et al, 2018) were leveraged to 192 improve scaffolding using MeDuSa (Bosi et al, 2015). The resulting R. idaeus genome assembly 193 is 300 Mbp in size, containing 2,145 scaffolds with a N50 of 638 Kb (Table 1) Table 2).…”

“…Rubus idaeus is a member of the economically important Rosaceae family that also includes 36 rose, peach, apple, cherry, pear, almond, strawberry, and blackberry. Up to now, the genomes of 37 several Rosaceae family members have been sequenced, including Rubus occidentalis (black 38 raspberry) (VanBuren et al, 2016, Malus x domestica (apple) (Daccord et al, 2017;39 Velasco et al, 2010), Prunus persica (peach) (Ahmad et al, 2011;Verde et al, 2013), Pyrus 40 bretschneideri (Chinese pear) and Pyrus communi (Chagne et al, 2014) (Chagné et al, 2014), 41…”

Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

“…The genomics era has revolutionized research on fruit tree species and of these genomes have recently been sequenced, or are currently being sequenced [1][2][3] . Nevertheless, although the cost for sequencing genomes has dropped considerably, obtaining high quality assemblies and annotations for complex plant genomes is still challenging 4 .…”