Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...
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