Chromosome-level assembly of the octoploid cloudberry ( Rubus chamaemorus )

We describe a chromosome-level genome assembly from an individual male plant of the cloudberry ( Rubus chamaemorus ). The haplotype-resolved assemblies contain one pseudo-haplotype spanning 1198 megabases and one pseudo-haplotype spanning 1161 megabases. Most of these two assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same BUSCO completeness score of 99.2%. Most BUSCO genes are duplicated in both pseudo-haplotypes, in line with the polyploid nature of the cloudberry genome. The assemblies contain 74,132 and 70,692 predicted protein-coding genes, respectively. Analysis of repetitive sequences classified ∼60% of each haplotype as repeats. Comparative synteny with red raspberry ( Rubus idaeus ) reveals a 4:1 chromosome correspondence, supporting an octoploid origin. Ks distributions and k-mer clustering indicate a recent polyploidization involving one divergent (β) and three closely related (α) subgenomes. Genome skimming data mapped to our assembly link the α-subgenomes to a putative hexaploid lineage related to Rubus arcticus , and the β-subgenome to Rubus pedatus , previously proposed as the maternal ancestor.