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 with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.

有效利用野生近缘种是克服遗传基础狭窄的栽培番茄遗传改良挑战的关键；然而，目前破译番茄野生物种高质量基因组的努力还不够。在这里，我们报告了来自九个野生物种和两个栽培品种的染色体规模番茄基因组，代表番茄分支番茄科。与之前发布的两个基因组一起，我们阐明了番茄的系统发育并构建了全节基因库。我们揭示了结构变异的景观，并提供了番茄野生近缘种基因组多样性的入口，从而能够发现具有增加现代栽培番茄产量潜力的野生番茄基因。基于图的基因组的构建可以实现基于结构变异的全基因组关联研究，识别与番茄风味相关性状和水果代谢物相关的大量信号。番茄超全基因组资源将加速这种全球重要作物的生物学研究和育种。