Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene…

• NS
  National Science Foundation

  Awards: IOS-1855585, 1855585
• NN
  National Natural Science Foundation of China

  Awards: 31991180, 32260763, 31860555, CARS-23, 2022001, 2021YFF1000100
• CA
  Chinese Academy of Agricultural Sciences
• CA
  Chinese Academy of Tropical Agricultural Sciences
• AA
  Anhui Agricultural University
• HU
  Hebei University
• UO
  University of California, Davis
• IO
  Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
• NK
  National Key Research and Development Program of China

  Awards: 2021YFF1000100, CARS-23, 2019YFA0906200
• XA
  Xinjiang Academy of Agricultural Sciences