The identification and annotation of expressed genes within the T. subterraneum genome assembly used high‐throughput whole genome RNA sequencing analyses to predict a total of 32 333 transcripts for 31 272 protein‐coding genes, with evidence for their expression across five different tissue types. The process‐involved annotations that combined evidence from transcriptome alignments obtained from protein homology and in silico gene prediction derived from different tissue types (roots, stem and peduncles, leaf and petioles, flowers and developing seeds) of cv. Daliak (Table S1). Phytozome and TrEMBL were the most informative databases for assigning functional annotations to subterranean clover proteins, with 29 157 (90.2%) and 29 278 (89.9%) proteins annotated, respectively (Table S2). In the draft TSUd_r1.1, the presence of 42 706 genes was predicted from in silico evidence using homology studies, domain searches and ab initio gene predictions. The reduction in genes annotated in the present study was achieved because the latter computational methods are unable to provide definitive evidence about which genes are actually expressed (Guigó et al., 2000; Wheelan and Boguski, 1998).