<p>Supplementary tables.</p>

These rearrangements pose challenges for precise karyotyping and the assembly of a genus pan-genome for crops and their wild relatives. <i>Lens culinaris</i>, an important cool-season legume primarily grown in India and Canada, is a cultivated species with six wild relatives. All seven <i>Lens</i> species exhibit distinct chromosomal arrangements, which affect introgression and complicate the development of an accurate karyotype for the genus.

Using gene synteny analysis between the cultivated <i>Lens</i> species and six wild relatives, we developed cross-species oligo-FISH (Fluorescent <i>in situ</i> hybridization) probes to <i>in situ</i> confirm genome assemblies and synteny. Chromosome spreads were used for oligo-FISH experiments, in which the DNA was denatured and a set of red and green oligo probes was hybridized to the metaphase chromosomes. The combination of both oligo sets/probes resulted in a distinct pattern for each <i>Lens</i> spp. chromosome, allowing the inference of a more robust karyotype for six <i>Lens</i> species.