T2T genome assembly of Rubus alceifolius Poir.

The genus Rubus serves as an ideal model for exploring plant genome evolution due to its complex polyploidization history, frequent interspecific hybridization, and exceptional adaptive capacity. Given its potential medicinal value and recognized invasive ecological threats,​the wild allotetraploid Rubus alceifolius Poir.​​ represents a scientifically important taxon. Here, we assembled a telomere-to-telomere gap-free genome assembly of R. alceifolius Poir. using PacBio HiFi, ONT, Hi-C and Illumina short reads sequencing. The assembly spans 462.05 Mb, anchored into 14 pseudochromosomes with a scaffold N50 of 33.09 Mb, and includes all 28 telomeric regions. Genome annotation revealed that 44.95% of the assembly comprises repetitive sequences, and 46,698 protein-coding genes were predicted, with 93.90% functionally annotated. Notably, a large-scale inversion structural variant spanning 12.44 Mb (6.65–19.09 Mb) was identified on chromosome Chr2 of the subgenomeA. This high-quality genome assembly fills a critical gap in genomic resources for polyploid Rubus species and provides an essential foundation for elucidating adaptive evolution mechanisms within the genus, as well as advancing molecular breeding strategies for raspberry improvement.