Subterranean clover is a diploid (2n = 2x = 16), predominantly inbreeding, annual species with a relatively small genome size of 540 Mbp (1C = 0.55 pg DNA; Vižintin et al., 2006) that can be readily hybridized, and exhibits wide diversity for both qualitative and quantitative agronomic and morphological characters (Ghamkhar et al., 2011). Within the genus Trifolium, it is established as a reference species for genetic and genomic studies. We reported a de novo draft genome assembly of the subterranean clover TSUd_r1.1, generated using a combination of long‐ and short‐read sequencing platforms (Figure S1) (Hirakawa et al., 2016). Genetic and genomic analyses of the internationally commercially important perennial legumes white clover and red clover are difficult, as they are outcrossing and have self‐incompatible fertilization, with white clover also being an allotetraploid (2n = 4x = 32) (Abberton and Marshall, 2005; Ghamkhar et al., 2011). As molecular markers developed for white and red clovers were readily transferable to subterranean clover (Ghamkhar et al., 2011), it is likely that subterranean clover QTLs and genes are applicable to these other species. Close synteny with the model legume, Medicago truncatula, also provides opportunities for genomic comparisons and the identification of candidate genes.