(a) Venn diagram of SNVs/InDels diversity of the cassava genomes of W14, KU50 and CAS36 sequenced in this study with comparison to the AM560 genome sequences previously released. The number of SNVs is listed and the number of InDels is shown in parentheses. (b) Chromosome in situ hybridization showing the repeated occurrence of 45S (Nucleolus organizer, NOR), LTR and chromosome numbers (2n=36) of cultivar KU50. (c) A CirCOS (http://circos.ca/) figure showing synteny between three paralogous cassava genomic regions and their putative orthologues present in R. communis and A. thaliana genomes. Coloured lines connect the cassava scaffolds to the A. thaliana chromosomes and R. communis scaffolds. The line distances across different scaffolds denote the similarities of the segments, with a longer line indicating a higher similarity. (d) Gene tree showing the divergence time of the wild ancestor subspecies to cultivars, referenced to neighbour species in the Euphorbiaceae family inferred from sequence comparison to 71 chloroplast genes from eight different plant species. Mtr: Medicago truncatula, Csa: Cucumis sativus, Ptr: Populus trichocarpa, Pni: Populus nigra, Ptd: Populus trichocarpa x Populus deltoids, Rco: Ricinus communis, Ees: Euphorbia esula, Jcu: Jatropha curcas, Mef-W14: Manihot esculenta ssp. flabellifolia (W14), Mes-KU50: Manihot esculenta ssp. esculenta (KU50), Mes-AM560: Manihot esculenta ssp. esculenta (cultivar AM560).