Abstract
Paliurus hemsleyanus Rehd., a deciduous shrub or small tree endemic to China, is valued for its hardiness, economic and ornamental importance, and widespread used as a rootstock for Chinese jujube (Ziziphus jujuba Mill.). Despite its ecological and economic significance, genomic resources for this genus remain limited. Here, we assemble a haplotype-resolved, telomere-to-telomere (T2T), gap-free genome of P. hemsleyanus (2n = 24), representing the genus Paliurus. The genome comprises two haplotypes of 306.65 Mb and 306.21 Mb, with contig N50 values of 24.91 Mb and 24.94 Mb, respectively. Each haplotype encodes over 29,000 protein-coding genes, with all centromeres and telomeres fully predicted. Allele-specific expression analysis reveals a positive correlation between gene expression divergence and sequence variation, indicating functional differentiation between haplotypes. Comparative genomic analysis shows relatively stable genome evolution within Rhamnaceae, with all examined extant species containing 12 chromosomes. Disease resistance (NLR) genes exhibit a root-preferred expression pattern, and allelic copies expressed more strongly than non-allelic ones between haplotypes. Ascorbic acid (AsA) metabolic genes show leaf-preferred expression; and moreover MDHAR genes exhibit Rhamnaceae-specific tandem duplications, suggesting lineage-specific adaptive evolution. This high-quality genome provides an essential resources for evolutionary studies, functional genomics, breeding, and the conservation of Rhamnaceae species.