The first draft genome assembly of the Australian subterranean clover variety, cv. Daliak, covers 85.4% of the estimated genome in eight pseudomolecules of 401.1 Mb length and was constructed using a linkage map consisting of 35 341 SNPs (Hirakawa et al., 2016). In this study, we evaluated genome mapping via scaffolding using de novo physical maps generated using the BioNano Genomics (BNG) Irys platform to improve the genome assembly. A total of 221.7 Gb (401× genome coverage) of filtered data (molecules >150 kb) was generated on the Irys instrument. After filtering out low‐quality single molecules, a total of 188.5 Gb (341× genome coverage) of data was included in the final BioNano‐based de novo physical map assembly. This physical map assembly consisted of 309 075 individual molecules and 468 consensus maps that spanned 512 Mb (93% genome coverage) with N50 of 1.4 Mb. Multiple contigs (264) from the first draft assembly coalesced into 97 super‐scaffolds (containing 43% of the total genome captured) (Figure 1). In the advanced assembly (Tsub_Refv2.0), the size of sequences longer than >1 Mb increased dramatically from 40 to 189 Mb. This resulted in a 1.4‐fold increase in the N50 with the total percentage of genome captured in pseudomolecules improving from 73 to 80% with a substantial reduction of sequence gaps (Table 1).