(a) Phylogenetic tree using the published predicted protein sequences for 13 legume genomes including the newly annotated Trifolium subterraneum L. and Arabidopsis thaliana. Mash v1.1 (preprint: http://biorxiv.org/content/early/2016/04/19/029827) was used to calculate a distance matrix and pairwise mutation distance estimation using the published whole genome sequences for all the legumes except the transcriptome assembly for Cajanus cajan as a whole genome assembly was not available. The phylogeny was constructed using UPGMA as implemented in the R‐package ‘phangorn’ v2.0.3. (b) Shared and unique gene clusters in A) Papilionoideae species and A. thaliana; B) Millettioid, Galegoid and Dalbergioid clade or and A. thaliana; C) Lotus, Trifoliums, Medicago and Cicers; D) Shared and unique genes in sub‐clover and red clover.