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

We describe a chromosome-level genome assembly from an individual male plant of the cloudberry (Rubus chamaemorus). The haplotype-resolved assemblies contain 1 pseudo-haplotype spanning 1,198 megabases and 1 pseudo-haplotype spanning 1161 megabases. Most of these 2 assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same Benchmarking Universal Single-Copy Orthologs (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, 1 set of 7 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. Significance statement Cloudberry cultivation has lagged due to limited genomic resources and an unresolved polyploid history. We present a haplotype-resolved, chromosome-scale assembly that resolves 4 homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry (Rubus idaeus). Genome-wide analyses support an octoploid architecture with 1 distinct 7-chromosome set (β) and a remaining α-set of 21 chromosomes with no resolvable internal subdivision. This reference provides a foundation for future work on polyploid origin, trait discovery, and breeding.