Gene family expansions and nodule-specific expression patterns reveal the recruitment of Beta-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 5,000 soybean RNA-Seq 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, NLP proteins, and GRAS transcription factors. Notably, we identified previously unreported {beta}-glucosidase and cytochrome P450 genes with high nodule-specific expression, suggesting their involvement as novel components of the nodulation machinery.