Telomere-to-telomere genome of Stylosanthes guianensis uncovers symbiotic adaptation to phosphorus-deficient soils.

BACKGROUND

Stylosanthes guianensis, a representative tropical legume, exhibits remarkable adaptation to low-phosphorus acidic soils. As a symbiotic species, it forms root nodule associations with rhizobia to fix atmospheric nitrogen, potentially enhancing phosphate use efficiency. This study aims to decipher the mechanisms linking root nodule symbiosis to low-phosphate adaptation in Stylosanthes guianensis.

RESULTS

We present the first gap-free, telomere-to-telomere genome of Stylosanthes guianensis (1.20 Gb), containing 82.28% repetitive sequences and 34,728 genes, with 99.30% BUSCO completeness and a 29.05 LTR Assembly Index score. Integrated genomic data and multi-omics analyses reveal a coordinated symbiotic strategy. Specifically, roots enhance flavonoid biosynthesis, likely driven by tandem duplication of chalcone reductase genes, to facilitate robust symbiont recruitment, while nodule development was regulated by a conserved network centered on the transcription factor NIN. In nodules, multiple phosphate starvation response pathways are activated, including enhanced phosphate transport and recycling, membrane lipid remodeling, and phosphate-conserving metabolic bypasses to support nitrogen fixation. Furthermore, co-upregulation of vitamin B6 and nitrogen assimilation pathways suggests a role in mitigating oxidative stress and sustaining metabolic balance.

CONCLUSIONS

This study reveals that root nodule symbiosis in Stylosanthes guianensis underpins a multifaceted adaptation to low-phosphate stress, integrating enhanced symbiotic signaling, conserved nodule development, reprogrammed phosphate metabolism, and improved antioxidant protection. These findings provide insights into stress-resilient symbiosis and a genomic foundation for improving nutrient efficiency in legumes.