Genomic and transcriptomic insights into legume-rhizobia symbiosis in the nitrogen-fixing tree Robinia pseudoacacia

Robinia pseudoacacia L. (black locust) is a nitrogen (N)-fixing legume tree with significant ecological and agricultural importance. Unlike well-studied herbaceous legumes, R. pseudoacacia is a perennial woody species, representing an understudied group of legume trees that establish symbiosis with Mesorhizobium. Understanding its genomic and transcriptional responses to nodulation provides key insights into N fixation in long-lived plants and their role in ecosystem N cycling. We assembled a high-quality 699.6-Mb reference genome and performed transcriptomic analyses comparing inoculated and noninoculated plants. Differential expression and co-expression network analyses revealed organ-specific regulatory pathways, identifying key genes associated with symbiosis, nutrient transport, and stress adaptation. Unlike Medicago truncatula, which predominantly responds to nodulation in roots, R. pseudoacacia exhibited stem-centered transcriptional reprogramming, with the majority of differentially expressed genes located in stems rather than in roots. Co-expression network analysis identified gene modules associated with "leghemoglobins", metal detoxification, and systemic nutrient allocation, highlighting a coordinated long-distance response to N fixation. This study establishes R. pseudoacacia as a genomic model for nodulating trees, providing essential resources for evolutionary, ecological, and applied research. These findings have significant implications for reforestation, phytoremediation, forestry, and sustainable N management, particularly in depleted, degraded, and contaminated soil ecosystems.