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<p><i>Paliurus hemsleyanus</i> 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 (<i>Ziziphus jujuba</i> 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 <i>P. hemsleyanus</i> (2n = 24), representing the genus <i>Paliurus</i>. 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.</p>

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Haplotype-resolved t2t genome of paliurus hemsleyanus provides insights into rhamnaceae evolution and genome biology

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月4日

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  • Shufeng Zhang,
  • Jingjing Guo,
  • Donghui Lin,
  • Jian Shen,
  • Zhongchen Zhang,
  • Yihan Yang,
  • Yunxin Lan,
  • Jiao Li,
  • Jin Zhao,
  • Yuan Li,
  • Yaolong Zhang,
  • Mengjun Liu,
  • Meng Yang

摘要

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.