A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.)

PLoS One. 2022 Mar 16;17(3):e0265096. doi: 10.1371/journal.pone.0265096. eCollection 2022.

Abstract

Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar 'Anitra' are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes
  • Genomics
  • Plant Breeding
  • Rubus* / genetics
  • Sequence Analysis, DNA

Grants and funding

Jahn Davik and Dag Røen received support from the Norwegian Research Council. Grant number 234312/E50. Daniel James Sargent acknowledges the core funding from the East Malling Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.