Chromosome-scale genome sequence assemblies of the ‘Autumn Bliss’ and ‘Malling Jewel’ cultivars of the highly heterozygous red raspberry (Rubus idaeus L.) derived from long-read Oxford Nanopore sequence data

• DOI: 10.1371/journal.pone.0285756
• Publication Date: 2023-05-16T18:11:06Z
• Authors: R. Jordan Price; Jahn Davik; Felicidad Fernand...; Helen J. Bates; Samantha Lynn; Charlotte F. Nellist; Matteo Buti; Dag Røen; Nada Šurbanovski; Muath Alsheikh; Richard J. Harrison; Daniel James Sargent
• Keywords: Rubus; Blowing a raspberry; Sequence (biology); BLISS; Nanopore

Red raspberry (Rubus idaeus L.) is an economically valuable soft-fruit species with a relatively small (~300 Mb) but highly heterozygous diploid (2n = 2x 14) genome. Chromosome-scale genome sequences are vital tool in unravelling the genetic complexity controlling traits of interest crop plants such as red raspberry, well for functional genomics, evolutionary studies, and pan-genomics diversity studies. In this study, we developed primocane fruiting variety ('Autumn Bliss') floricane ('Malling Jewel'). The use long-read Oxford Nanopore Technologies sequencing data yielded long read lengths that permitted resolved two cultivars to be assembled. de novo assemblies 'Malling Jewel' 'Autumn Bliss' contained 79 136 contigs respectively, 263.0 Mb 265.5 assembly could anchored unambiguously previously published sequence cultivar 'Anitra'. Single copy ortholog analysis (BUSCO) revealed high levels completeness both genomes sequenced, 97.4% identified 97.7% Jewel'. density repetitive was significantly higher than centromeric telomeric regions were assemblies. A total 42,823 protein coding assembly, whilst 43,027 assembly. These chromosome-scale represent excellent genomics resource particularly around less complete 'Anitra' sequence.