Haplotype-resolved T2T genome assembly of the pear cultivar 'Danxiahong'.

Pear (Pyrus L) is one of the most significant fruit crops globally, recognized for its substantial economic value and potential health benefits. 'Danxiahong' is an elite pear cultivar in the north of China, characterized by its flushed fruit skin and excellent inner quality. In this study, we utilized PacBio HiFi long reads, Hi-C reads and second-generation sequencing data to assemble the genome of 'Danxiahong'. Two telomere-to-telomere gap-free and haplotype-resolved pear genomes were successfully assembled, with the sizes of 495.37 Mb and 501.60 Mb, and contig N50 of 28.97 Mb and 29.32 Mb. Approximately 62.50% and 62.76% repeat sequences were mapped to the 17 chromosomes for each haplotype. Gene annotations analysis identified a total of 39,936 genes in Hap1 and 39,707 genes in Hap2, respectively. The haplotype-resolved genome of 'Danxiahong' significantly contributes to the investigation of genes and molecular mechanisms related to fruit quality, while also facilitating the Multi-Omics analysis, such as comparative genomics, transcriptomics, proteomics, and allelic expression research.