Effective utilization of wild relatives is key to overcome challenges in genetic improvement of cultivated tomato that has a narrow genetic basis; however, current efforts on deciphering 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 (SVs) and provide entry to the genomic diversity among tomato wild relatives, empowering the discovery of a cytochrome P450 gene possessing potential for yield increase in modern cultivated tomatoes. Graph-based tomato genome enables SV-based genome-wide association studies in a large population of tomato, identifying numerous signals associated with 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:
- Genome assembly
- Genome annotation
- Pan-genome
- Phylogenetic analyses
- Structural variation
- Graph-based genome
- Genome-wide association studies
We have implemented a web-based database hosting the genoimc datsets and provide a series of user-friendly tools. Please http://caastomato.biocloud.net/home for more details.
Hongbo Li (lihongbo_solab@163.com)
Ning Li (lining@xaas.ac.cn)
Qiang He (qiangh@163.com)
Qinghui Yu (yuqinghui@xaas.ac.cn)