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Background <p>Perennial leguminous shrubs of the genus <i>Caragana</i> play key roles in arid and semi-arid ecosystems, contributing to ecological restoration, nitrogen fixation, and bioenergy production. However, the genomic basis underlying their adaptation to arid environments remains insufficiently understood.</p> Results <p>Here, we generate chromosome-scale genome assemblies for 14 representative <i>Caragana</i> species, including a near telomere-to-telomere assembly of <i>Caragana korshinskii</i> (NMCN13). Using these genomes, we construct a graph-based pan-genome and identify extensive genomic variation, including 801,351 structural variants and 104,404 presence-absence variations. Comparative analyses identify clade-specific gene family expansions enriched in stress-related pathways, particularly secondary metabolism. We further identify two candidate drought-responsive genes, <i>CkoERF1</i> and <i>CkoWAKL</i>, whose functions are supported by heterologous overexpression in <i>Arabidopsis thaliana</i> and alfalfa, demonstrating enhanced drought-response phenotypes. Transposable element analyses indicate that variation in LTR retrotransposon abundance contributes to genome size diversity across species. Notably, we find that some key symbiosis-related genes, for example, <i>NIN</i>, <i>DMI1</i>, <i>DMI2</i>, and <i>NSP1</i>, are conserved across all species, suggesting a stable genetic basis for nitrogen fixation.</p> Conclusions <p>This study provides high-quality genomic resources and a comprehensive pan-genomic framework for <i>Caragana</i>. Our findings offer new insights into genome evolution, environmental adaptation, and drought tolerance mechanisms, and establish a foundation for future functional genomics and breeding efforts in leguminous shrubs.</p>

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Pan-genome analysis of Caragana reveals genomic mechanisms of drought adaptation of leguminous shrubs to arid environments

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年8月1日

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  • Jiaxing Song,
  • Jie An,
  • Houyin Xia,
  • Wanjiang Li,
  • Jingdian Hu,
  • Qian Li,
  • Chenjian Li,
  • Xiaoxia Shen,
  • Hong Cheng,
  • Yi Zhou,
  • Tianming Hu,
  • Peizhi Yang

摘要

Background

Perennial leguminous shrubs of the genus Caragana play key roles in arid and semi-arid ecosystems, contributing to ecological restoration, nitrogen fixation, and bioenergy production. However, the genomic basis underlying their adaptation to arid environments remains insufficiently understood.

Results

Here, we generate chromosome-scale genome assemblies for 14 representative Caragana species, including a near telomere-to-telomere assembly of Caragana korshinskii (NMCN13). Using these genomes, we construct a graph-based pan-genome and identify extensive genomic variation, including 801,351 structural variants and 104,404 presence-absence variations. Comparative analyses identify clade-specific gene family expansions enriched in stress-related pathways, particularly secondary metabolism. We further identify two candidate drought-responsive genes, CkoERF1 and CkoWAKL, whose functions are supported by heterologous overexpression in Arabidopsis thaliana and alfalfa, demonstrating enhanced drought-response phenotypes. Transposable element analyses indicate that variation in LTR retrotransposon abundance contributes to genome size diversity across species. Notably, we find that some key symbiosis-related genes, for example, NIN, DMI1, DMI2, and NSP1, are conserved across all species, suggesting a stable genetic basis for nitrogen fixation.

Conclusions

This study provides high-quality genomic resources and a comprehensive pan-genomic framework for Caragana. Our findings offer new insights into genome evolution, environmental adaptation, and drought tolerance mechanisms, and establish a foundation for future functional genomics and breeding efforts in leguminous shrubs.