The advanced assembly was functionally characterized by assigning gene ontology (GO) terms to proteins by manually transferring the GO terms for Swiss‐Prot IDs using the UniProt‐GOA database (Huntley et al., 2015). All these protein‐coding genes/transcripts were grouped into the three main GO categories: biological processes, molecular function and cellular components. A total of 21 210 (65.6%) of the subterranean clover protein‐coding genes/transcripts were assigned GO terms (Table S1). Of the 131 324 GO terms identified, 5,648 appear only once. There are 1013 GO terms appearing between 50 and 200 times with a total sum of 35 383 (Figure S2).