ArticleThe Journal of heredity2026
The origin of the octoploid cloudberry (Rubus chamaemorus) genome is the result of multiple and complex polyploidization events.
Article in The Journal of heredity, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
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.
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