Fig. 1: Visualizations of genome compositions of A. hypogaea, A. monticola and hybrids derived from the peanut’s ancestors.

a–e, Overviews of genetic exchange between ancestral A and B genomes; f,g, visualization of fine-scale exchange at the ends of chromosomes. In a–e, data are of log₂-transformed values of ratios of mapping densities of whole-genome sequences onto 17,373 orthologous A/B gene pairs from A. ipaensis and A. duranensis, ordered according to chromosome number and position in A. ipaensis. Where values cluster around zero, as is the case in the diploid hybrid in a, A and B genes are present in equal number and are unaltered by genetic flux between them; in tetraploid genotypes this indicates a genome structure of AABB. Deviations from zero indicate genetic flux between the orthologous gene pairs, or complete replacement of A genes by B, or vice versa. b, The ninth generation tetraploid hybrid shows such deviations, with a change in genome structure from AABB to AAAA for chromosomes A04/B04 and the upper regions of B07/A08. c–e, These patterns are very different from those of A. monticola and A. hypogaea, which are similar to each other (and throughout diverse genotypes). Note deviations are mostly at chromosome ends. f,g, Fine-scale recombination (fingerprints) between A and B subgenomes are shown in two distal chromosome regions in which the genome structure approximates AAAA; the presence of SNPs characteristic of the ancestral B that form barcode-like patterns that are uniform in all A. monticola and A. hypogaea are observed. These patterns emphasize the similarities between A. monticola and A. hypogaea and favor a single polyploid origin (Supplementary Fig. 25; dataset 4a in ref. ²⁵).