Electronic supplementary material for the paper "The genome sequence of segmental allotetraploid peanut Arachis hypogaea", Bertioli et al., 2019. Materials include: Information on the expression of homeologous gene pairs; Key to germplasm used in the associated study; Basecalls at assessed genomic positions in tetraploid assembly; Files used for the visualization of genome structure variations; Data for visualization of homeologous recombination between corresponding chromosomes; and information about genotyping and phenotypic of induced allotetraploid lines.