Comparative analyses across the Papilionoideae using the published whole genome sequences for 13 legumes and the Tsub_Refv2.0 (Figure 5a and b; Table S14) revealed an overlap of 12 170 orthologous gene clusters between Papilionoideae and Arabidopsis thaliana as the outgroup species. Within the Papilionoideae, the number of orthologous gene clusters specific to galegoid (Lotus japonicus, Trifolium pratense, T. subterraneum, M. truncatula and Cicer arietinum), millettioid (Glycine max, Cajanus cajan, Vigna radiata, V. angularis and Phaseolus vulgaris) and dalbergoid (Arachis ipaensis and A. duranensis) was 10 873, 7976 and 4004, respectively. There were 3171 orthologous gene clusters in common among galegoid, millettioid and dalbergoid species.