Here, we sequence and de novo assemble chromosome-scale genomes of nine wild species and two cultivated accessions of tomato, and constructe a super-pangenome, revealing phylogenetic relationships and structural variation among Solanum section Lycopersicon. Comparative analyses reveal extensive variation among the toamto wild species, empowering the identification of a wild-type allele presenting potential values for yield improvement in modern cultivated tomatoes.

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 see http://caastomato.biocloud.net/home for more details.

Hongbo Li ([email protected])

Ning Li ([email protected])

Qiang He ([email protected])