Gene family expansions and nodule-specific expression patterns reveal the recruitment of β-glucosidases and cytochrome P450 genes to nodulation in soybean

Abstract Nodulation is a symbiotic interaction between legumes and rhizobia that is essential for biological nitrogen fixation and regulated by complex gene networks, which are partially shaped by whole-genome duplication (WGD) events. Although many core nodulation genes have been identified, the contribution of lineage-specific gene expansions and WGD-derived duplicates remains poorly understood. In this study, we performed a genome-wide analysis of gene family expansions in legumes and integrated expression data from over 5000 soybean RNA-sequencing samples to identify genes involved in nodulation. Our analysis not only recovered well-characterized nodulation genes among the most expanded families but also revealed several differentially expressed genes in nodules, including nodulins, aspartic proteases, nodule inception-like proteins and GRAS transcription factors. Notably, we identified previously unreported β-glucosidase and cytochrome P450 genes with high nodule-specific expression, suggesting their involvement as novel components of the nodulation machinery.