Independent domestication and cultivation histories of two West African indigenous fonio millet crops : pipeline and codes

Crop evolutionary history and domestication processes are key issues for better conservation and effective use of crop genetic diversity. In Western Africa, two small indigenous grain cereals are found, black and white fonio (Digitaria exilis and Digitaria iburua respectively). The relationship between these two cultivated crops and wild Digitaria species is still unclear. We analysed whole genome sequences of 265 accessions comprising the two cultivated species and their closely wild relatives. We used different complementary methods and genomic approaches to unravel the domestication history of these fonio millets, which is key to support a process of valorisation of these native species while preserving the diversity necessary for future adaptations. We provide here the scripts for the bioinformatics analysis, the custom R code used to perform the analyses and input files associated. The scripts support the following article: Kaczmarek, T., Cubry, P., Champion, L. et al. Independent domestication and cultivation histories of two West African indigenous fonio millet crops. Nat Commun 16, 4067 (2025). https://doi.org/10.1038/s41467-025-59454-2