lizhi-git/tomatosuperpangenome

Here, we sequence and de novo assemble chromosome-scale genomes of nine wild species and two cultivated accessions of tomato and constructed a pan-genome, revealing phylogenetic relationships and structural variation among Lycopersicon

TomatoSuperPanGenome

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.

Content

Pipelines and relevant scripts for:

• Genome assembly
• Genome annotation
• Pan-genome
• Phylogenetic analyses
• Structural variation
• Graph-based genome
• Genome-wide association studies

The website

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.

Citation

Contacts

Hongbo Li ([email protected])

Ning Li ([email protected])

Qiang He ([email protected])

Qinghui Yu ([email protected])