We compared the candidate contigs with the available annotation of the yam transcriptome reference . Thus, we retrieved some genes corresponding to putative targets for selection during yam domestication. In particular, among the genes annotated for the candidate genes, we identified five candidate contigs that were relevant in the light of yam domestication (Fig. 3 and Additional file 2: Table S5). These five candidate contigs showed strong diversity loss in the cultivated group compared to the wild species (Additional file 2: Figure S7). A candidate contig was a putative SCARECROW-LIKE gene involved in root development [42, 43]. Two other genes were associated with the earliest stages of starch biosynthesis and storage i.e., genes coding for the sucrose synthase 4  and the sucrose-phosphate synthase 1 . We also identified two genes associated with growth and phototropism, respectively: Ethylene Insensitive 4 genes (EIN4)  and Phototropin 2 gene (Phot2, . The 998 candidate contigs were significantly enriched for a total of 21 significant GO terms (Additional file 2: Table S6). When we restricted our analysis to the 81 candidate contigs detected by at least two methods, we obtained nine significant GO terms (Additional file 2: Table S7). The most significant GO terms were identical whether we considered all the candidate contigs or only the 81 candidate contigs. The set of GO terms found across these two enrichment tests was associated with dehydrogenase and oxidoreductase (NADH DH) activities (Fig. 4).Fig. 3Key genes associated with yam domestication. SCARECROW-LIKE, Phot2, EIN4, SUS4 and SPS1 are some interesting genes probably selected during domestication Fig. 4TreeMap view of the 10 most significant “Go Terms” identified. The 10 most significant GO terms were reported with their respective p-values. We group them in 4 major clusters: “oxidase activity” in green, “transferase activity” in blue, “catalytic activity” in pink. “cofactor binding” in yellow