The origin of the octoploid cloudberry ( Rubus chamaemorus ) genome is the result of multiple and complex polyploidization events

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. Across k-mer composition, synonymous divergence, and genome-wide gene-tree analyses, one set of seven chromosomes is consistently distinct (β), while the remaining 21 (3×7) chromosomes form an α set with no resolvable internal subdivision. These results are consistent with a complex polyploid origin of the cloudberry genome, involving a combination of allopolyploid and autopolyploid processes.