<p>Nature Genetics, Published online: 24 February 2026; <a href="https://www.nature.com/articles/s41588-026-02510-4">doi:10.1038/s41588-026-02510-4</a></p>We constructed a super pangenome for the tomato, incorporating 20 newly assembled telomere-to-telomere (T2T) genomes and 27 previously published genomes. This comprehensive, genus-wide resource enables insight into tomato pan-centromere diversity and evolution, provides a catalog of structural variants and molecular markers linked to salinity tolerance, and led to the discovery of an immune receptor that confers resistance to fungal infection.