biostudies-literatureUnknown16Nan HThe MADS-box gene family plays a central role in plant development and adaptation, yet its evolutionary history in legumes is remarkably complex. In this study, we performed a pangenomic analysis across 52 legume species, identifying 4,872 MADS-box genes and reconstructing their phylogeny into 16 subfamilies. Our analysis uncovered a pervasive dualistic evolutionary model driven by distinct duplication mechanisms. Structurally, the genes fall into two categories: the compact, intron-poor Type I and the complex, intron-rich Type II. We demonstrate that whole-genome duplication (WGD) serves as the major driver (42.2%) behind the expansion of the conserved core genome, which includes key floral regulators such as the "ABCDE model" genes. These WGD-derived genes are under strong purifying seleFrontiers in plant science1740598https://www.ebi.ac.uk/biostudies/studies/S-EPMC12853372biostudies-literatureDualistic MADS-box evolution forged legume diversity post-WGD.PMC12853372Zhang JZou MGuo XKou KNan HChen XShang EfalseDualistic MADS-box evolution forged legume diversity post-WGD.The MADS-box gene family plays a central role in plant development and adaptation, yet its evolutionary history in legumes is remarkably complex. In this study, we performed a pangenomic analysis across 52 legume species, identifying 4,872 MADS-box genes and reconstructing their phylogeny into 16 subfamilies. Our analysis uncovered a pervasive dualistic evolutionary model driven by distinct duplication mechanisms. Structurally, the genes fall into two categories: the compact, intron-poor Type I and the complex, intron-rich Type II. We demonstrate that whole-genome duplication (WGD) serves as the major driver (42.2%) behind the expansion of the conserved core genome, which includes key floral regulators such as the "ABCDE model" genes. These WGD-derived genes are under strong purifying sele2025-01-01T00:00:00Z20252026-06-20T03:20:07.986Z2026-06-20T03:09:44.308ZS-EPMC128533724162633310.3389/fpls.2025.1740598