Extended Data Fig. 1: Genome type-level pangenomes for the AA, BB, CC, and DD types.

a) A growth histogram relative to the cumulative number of (sub)genomes on the x-axis is shown for the AA, BB, CC, and DD pangenomes, respectively. Sequences shared by all (sub)genomes represent the core pangenome (green), partially shared sequences represent the dispensable pangenome (ochre). b) Pangenome visualization of the translocation on chromosome 1 C in O. alta and O. grandiglumis. The red arrow points to the chromosomal region corresponding to an unbalanced translocation of a portion of Chr3 on Chr1 (see also panel c). This chromosomal rearrangement is present in O. alta and O. grandiglumis (red box) and absent from the other CC types used to build the CC pangenome (that is O. officinalis, O. minuta, O. malampuzhaensis and O. latifolia). c) The riparian plot shows the synteny between O. sativa (AA), O. alta (CC), O. grandiglumis (CC), O. latifolia (CC) and L. perrieri chromosomal regions. The red box highlights the duplication and translocation of a portion of Chr3 on Chr1 in O. alta and O. grandiglumis.