Kobayashi, M. J.; Chigira, O.; Widiyatno, W.; Na'iem, M.; Tani, N.

Whole-genome duplication (WGD) has played a fundamental role in shaping plant genome evolution, yet the timing and independence of WGD events in major Fabaceae subfamilies, including Caesalpinioideae and Papilionoideae, remain debated. Here, we present a chromosome-level genome assembly of the tropical mimosoid tree Falcataria falcata within Caesalpinioideae and investigate the evolutionary consequences of ancient polyploidy. The assembled genome spans 614.9 Mb with 13 chromosome-level scaffolds and 99.6% completeness based on BUSCO assessment, providing a high-quality resource for comparative genomics. Synteny analyses revealed conserved macrosyntenic structures shared across Caesalpinioideae, consistent with an ancestral WGD event predating lineage diversification. In contrast, analyses of synonymous substitution rates (Ks) and phylogenetic relationships of conserved duplicate genes support independent WGD events in Caesalpinioideae and Papilionoideae. We further show that lineage-specific variation in synonymous substitution rates is negatively associated with the retention of WGD-derived duplicates following the ancestral WGD in Caesalpinioideae, suggesting that evolutionary rate heterogeneity plays a key role in post-WGD genome evolution. In addition, recent gene duplicates that arose independently in each lineage after WGD exhibit elevated Ka/Ks ratios and are predominantly associated with defense responses to diverse biotic stresses, suggesting more rapid sequence evolution and functional divergence compared with WGD-derived duplicates. Together, our results reveal how ancient WGD, lineage-specific evolutionary rates, and subsequent gene duplication have jointly structured genome evolution in Fabaceae. The genome of F. falcata provides a valuable resource for understanding the long-term evolutionary consequences of polyploidy and the diversification of ecological adaptations in legumes.