Additional file 1:We assess if the mapping of genomic DNA reads on a transcriptome reference could impact SNP calling in our special case. Table S1. Summary of mapping and SNP calling using simulated data. (DOCX 15 kb) Additional file 2:Molecular basis of African yam domestication: analyses of selection point to starch biosynthesis, root development and photosynthesis related genes. Table S1. Passport data of plant material collected from Benin. Table S2. Metric information of data filtering and mapping. Table S3. Mean Nucleotide diversity (π) and polymorphism (ɵ). Table S4. List of the contigs detected as selected by at least one method. Table S5. Remarkable candidate genes showing selection signature. Table S6. Gene Ontology (GO) terms significantly enriched (p-value ≤ 0.05) among the 998 candidate contigs. Table S7. Gene Ontology (GO) terms significantly enriched (p-value ≤ 0.05) among the 81 candidates contigs detected by a least two methods. Figure S1. Cross-entropy calculated using sNMF (Frichot et al., 2014) for K = 1 to 6. Ten repetitions of the run were done. Figure S2. Intra-contigs linkage disequilibrium (LD) as a function of physical distance between SNPs pairs from 1% of all contigs. Figure S3. Venn Diagram comparing the candidate contigs obtained using the 4 methods. Figure S4. Distribution of Tajima’s D value calculated for D. abyssinica (a) and D. praehensilis (b). Figure S5. Comparison of diversity lost. Figure S6. Variance explained by PCA axis (a) and distribution of Mahalanobis distance (b) from PCAdapt. Figure S7. Nucleotide diversity within five candidate contigs for cultivated and the wild species (XLSX 45 kb)