Genes representing tissue‐enriched clusters were subjected to GO enrichment analysis to further characterize and identify over‐represented functional groups in subterranean clover using REVIGO web server (Supek et al., 2011) to graphically represent the results. The scatterplot depicting leaf‐enriched cluster (Cluster 2) showed enrichment for genes associated with photosynthesis, transport and response to stimulus (Figure 4b; Table S11). The flower‐enriched cluster (1) showed a concentration of genes associated with the processes of nitrogen compound cellular biosynthesis, multicellular organismal organization and development (Table S12). The stem‐ and peduncle‐enriched cluster (3) displayed a high representation of genes associated with response to stimulus, stress, oxidation‐reduction process, transport and signal transduction. The root‐enriched cluster (5) had a high representation of genes associated with response to stress, stimulus, nutrient levels, transport and nitrate metabolism. Clearly, the GO enrichment analyses of tissue‐enriched clusters showed over‐representation of predicted classes of genes in different tissue types and thereby validated our tissue‐enriched gene co‐expression clusters. Additionally, putative genes‐encoding enzymes in subterranean clover were assigned to various pathways in the KEGG database using BLASTKOALA (Kanehisa et al., 2016). This analysis distributed 4,094 genes‐encoding enzymes (12.7%) into 133 different KEGG pathways (Figure S3; Table S13).