Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Autor: Ning Li, Qiang He, Juan Wang, Baike Wang, Jiantao Zhao, Shaoyong Huang, Tao Yang, Yaping Tang, Shengbao Yang, Patiguli Aisimutuola, Ruiqiang Xu, Jiahui Hu, Chunping Jia, Kai Ma, Zhiqiang Li, Fangling Jiang, Jie Gao, Haiyan Lan, Yongfeng Zhou, Xinyan Zhang, Sanwen Huang, Zhangjun Fei, Huan Wang, Hongbo Li, Qinghui Yu
Rok vydání: 2023
Předmět:
Zdroj: Nature Genetics. 55:852-860
ISSN: 1546-1718
1061-4036
Popis: 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.
Databáze: OpenAIRE
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