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

Summary 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.