Our analysis predicted genome-wide targets for transcription factors, including novel regulators identified by DRMN and previously known regulators of root nodulation, such as NIN, NF-YA1/NF-YB1, and CYCLOPS. For example, MTG-LASSO analysis predicted NIN as a direct target of SHY2 and MTF1, and FLOT4, required for infection thread formation, as a target of IBM1 [46]. This evidence concerns the gene PRSS3 and infection.