Gene expression and regulatory networks provide new insights into the similarity between nitrogen fixing and arbuscular mycorrhizal symbioses.

Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbuscular mycorrhizal symbiosis (AMS). A growing number of symbiosis-regulated genes have been characterized through either genetic analysis or phylogenomic profiling. However, the underlying similarities and specificities of the transcription regulatory machinery in AMS and NFS remain largely unclarified. Here, we systematically profiled the gene expression changes in three legume species, namely Medicago truncatula, Glycine max, and Lotus japonicus, during AMS and NFS. Additionally, we investigated gene expression changes in three non-legume plants, Solanum lycopersicum, Zea mays, and Oryza sativa, during AMS. We identified thousands of genes that were activated by AMS or NFS in their respective host plants. Through comparative genomics analysis, we systematically explored the conservation and specificity of genes responsive to AMS or NFS. Employing M. truncatula and G. max as illustrative cases, we harnessed the XGboost machine-learning model to construct co-expression-based gene regulatory networks for AMS and NFS within these two species. Through this approach, we successfully illuminated the similarities and unique features of the two symbiotic types at the gene regulatory network level. Further, utilizing known symbiosis genes as queries, we pinpointed a multitude of genes that are intimately associated with AMS and NFS. Overall, via in-depth gene expression profiling and regulatory network analysis, our results indicate that, while NFS in legumes has regulatory circuits similar to those of AMS, there exist certain symbiosis type-specific molecular components.