Pan-genome analysis of Caragana reveals genomic mechanisms of drought adaptation of leguminous shrubs to arid environments.
4 affiliations
- 1College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- 2Key Laboratory of Ministry of Education of Grassland Resources and Ecology of Western Arid Region, Key Laboratory of Grassland Resources and Ecology of Xinjiang, College of Grassland Science, Xinjiang Agricultural University, Urumqi, 830052, China.
- 3School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia.
- 4College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China. [email protected].
Abstract
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.
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BibTeX
@article{song2026pangenome,
title = {{Pan-genome analysis of Caragana reveals genomic mechanisms of drought adaptation of leguminous shrubs to arid environments.}},
author = {Jiaxing Song and Jie An and Houyin Xia and Wanjiang Li and Jingdian Hu and Qian Li and Chenjian Li and Xiaoxia Shen and Hong Cheng and Yi Zhou and Tianming Hu and Peizhi Yang},
journal = {Genome biology},
year = {2026},
month = aug,
doi = {10.1186/s13059-026-04230-8},
url = {https://europepmc.org/article/MED/42958427},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Pan-genome analysis of Caragana reveals genomic mechanisms of drought adaptation of leguminous shrubs to arid environments.
AU - Jiaxing Song
AU - Jie An
AU - Houyin Xia
AU - Wanjiang Li
AU - Jingdian Hu
AU - Qian Li
AU - Chenjian Li
AU - Xiaoxia Shen
AU - Hong Cheng
AU - Yi Zhou
AU - Tianming Hu
AU - Peizhi Yang
PY - 2026
DA - 2026/08/01
JO - Genome biology
DO - 10.1186/s13059-026-04230-8
UR - https://europepmc.org/article/MED/42958427
AB - 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.
SN - 1474-7596
SN - 1474-760X
ER -