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

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. 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. 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.