Fig. 2: Structural variation generated by deletions and recombination between ancestral genomes (or subgenomes) of A. hypogaea.

a–c, Genetic exchange between Arahy.04 and Arahy.14 in three A. hypogaea, visualized by mapping the densities of short-read whole-genome sequences onto A. duranensis and A. ipaensis (normalized values, in blue and red respectively; distances scaled to Arahy.14). Where mapping densities cluster around the expected value of one, the genome composition is AABB. Where mapping densities on one genome increase to approximately two and on the other genome decrease to near zero, the genome composition is better described as AAAA or BBBB. Mapping densities decrease to around zero on one genome and remain around one on the other indicate a deletion (common in b). d, A panel of 68 representative diverse genotypes in a region of Arahy.04 and Arahy.14 in which hypervariability has been created by differential recombination between subgenomes. The panel represents a heat map of log₂-transformed ratios of mapping densities on the B and A genomes; blue represents AAAA and red represents BBBB, Tif., PI and Chib. are the genotypes repesented in a–c, respectively (for full visualizations, see dataset 4b in ref. ²⁵).