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

文献类型： 外文期刊

第一作者： Li, Ning

作者： Li, Ning;Wang, Juan;Wang, Baike;Huang, Shaoyong;Yang, Tao;Tang, Yaping;Yang, Shengbao;Aisimutuola, Patiguli;Xu, Ruiqiang;Hu, Jiahui;Jia, Chunping;Ma, Kai;Yu, Qinghui;He, Qiang;Zhao, Jiantao;Zhou, Yongfeng;Zhang, Xinyan;Huang, Sanwen;Li, Hongbo;Huang, Shaoyong;Xu, Ruiqiang;Hu, Jiahui;Gao, Jie;Jia, Chunping;Lan, Haiyan;Li, Zhiqiang;Jiang, Fangling;Fei, Zhangjun;Fei, Zhangjun;Wang, Huan

作者机构：

期刊名称：NATURE GENETICS （ 影响因子：30.8； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2023 年 55 卷 5 期

页码：

收录情况： SCI

摘要： 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. A tomato super-pangenome constructed using chromosome-scale genomes of nine wild species and two cultivated accessions highlights genomic diversity and structural variation across wild and cultivated tomatoes.

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