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.
Pipelines and relevant scripts for:
We have implemented a web-based database hosting the genoimc datsets and provide a series of user-friendly tools. Please visit http://caastomato.biocloud.net/home for more details.
Li, N., He, Q., Wang, J. et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat Genet 55, 852–860 (2023). https://doi.org/10.1038/s41588-023-01340-y
The genomic data has also been deposited in https://github.com/HongboDoll/TomatoSuperPanGenome/releases, in the case you encounter problems accessing the website.
Hongbo Li (lihongbo_solab@163.com)
Ning Li (lining@xaas.ac.cn)
Qiang He (qiangh@163.com)
Qinghui Yu (yuqinghui@xaas.ac.cn)