To find Trifolium‐specific genes among the galegoids, we identified 18 131 genes representing 24.3% of the total 74 556 genes using BLAST searches (Table S15). This proportion is higher than reported in chickpea (10%; Garg et al., 2011; Jain et al., 2013) Arabidopsis (4.9%; Lin et al., 2010) and rice (17.4%; Campbell et al., 2007). Trifolium‐specific gene clusters are a source of unique genes controlling important traits as drought tolerance, and disease resistance. Within the genus Trifolium, similar BLAST searches identified 6,325 (19.6%) and 11 806 (28.0%) genes as subterranean‐clover‐specific and red‐clover‐specific genes, respectively (Tables S16 and S17). These candidate subterranean‐clover‐specific genes could be mined further for such key traits as geocarpy and other factors related to the grazing tolerance of subterranean clover. Examining orthologous gene clusters provides an important foundation for comparative biology and functional inference in subterranean clover, because genes with simple orthologous relationships often have conserved functions, whereas genes duplicated more recently relative to speciation often underlie functional diversification. Comparative genomic analysis of the advanced subterranean assembly with the model legume, Medicago truncatula, showed close synteny and extensive collinearity of large sequence blocks (Figure 6). This provides opportunities for genomic comparisons and translation to identify candidate genes for traits of interest in the two species.