Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears.

Pears (Pyrus spp.) are self-incompatible crops with broad genetic diversity. High heterozygosity and technical limitations result in gaps within reference genomes. Our study presents the telomere-to-telomere, haplotype-resolved genomes of a representative Asian pear 'Dangshansuli' (Pyrus bretschneideri) and a European pear 'Max Red Bartlett' (Pyrus communis). Haplotype-specific genes exhibited notable differences from biallelic genes regarding transposable content, methylation patterns and expression levels. Allele-specific expression analysis suggested that the dominance effect is vital in the formation of fruit quality of pears. Population analysis of 362 accessions revealed that interspecific introgression increased pear diversity. We constructed a graph-based genome and identified structural variations associated with agronomic traits. A 286-bp insertion in the promoter region, along with differential expression of PyACS1, was identified between Asian and European pears, which exhibit distinct fruit-softening characteristics. Further experiments demonstrated the role of PyACS1 in fruit softening. Overall, this study provided insights into genetic variation and will facilitate pear improvement.