A phased telomere-to-telomere genome of Rosa wichuraiana ‘Basye’s Thornless’, a key progenitor for modern rose breeding

Rosa wichuraiana ‘Basye’s Thornless’ (BT) is a critical diploid germplasm in rose genetics and breeding programmes, prized for its superior traits including thornlessness, disease resistance, and vigorous root-sprouting capacity. Here, we present a telomere-to-telomere (T2T) haplotype-resolved genome assembly of BT generated using PacBio HiFi long reads, Oxford Nanopore Technologies ultra-long reads, and Hi-C chromatin conformation capture data. The final assembly spans 978.2 Mb and is anchored to 16 contiguous scaffolds, representing 14 chromosome-scale sequences corresponding to two complete haplotypes of seven chromosome pairs with six gaps, alongside the chloroplast and mitochondrial genomes. The N50 values of contig and scaffold are 67.9 Mb and 68.1 Mb, respectively. Assessment of assembly quality revealed a BUSCO completeness score of 99.0%, a consensus quality value (QV) of 68.11, and functional annotation of 95.6% among 67,611 predicted protein-coding genes, collectively confirming a high-quality, reference-grade assembly. Repetitive elements constitute 60.1% of the genome, predominantly composed of long terminal repeat (LTR) retrotransposons. There are 25,475 syntenic homologous gene pairs with extensive structural variation detected between the two haplotypes including 1,089,143 single-nucleotide polymorphisms (SNPs), 62 inversions, and 587 translocations. The BT genome features approximately 219 Mb of highly diverged regions, with chromosome 3 showing the highest genome heterozygosity by sequence length (~6.5%) and one 2.27 Mb inversion. These findings underscore both the high heterozygosity of the BT genome and the importance of haplotype-resolved assembly in capturing allelic diversity in roses.