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Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
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 f...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group US
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10181942/ https://www.ncbi.nlm.nih.gov/pubmed/37024581 http://dx.doi.org/10.1038/s41588-023-01340-y |
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author | Li, Ning He, Qiang Wang, Juan Wang, Baike Zhao, Jiantao Huang, Shaoyong Yang, Tao Tang, Yaping Yang, Shengbao Aisimutuola, Patiguli Xu, Ruiqiang Hu, Jiahui Jia, Chunping Ma, Kai Li, Zhiqiang Jiang, Fangling Gao, Jie Lan, Haiyan Zhou, Yongfeng Zhang, Xinyan Huang, Sanwen Fei, Zhangjun Wang, Huan Li, Hongbo Yu, Qinghui |
author_facet | Li, Ning He, Qiang Wang, Juan Wang, Baike Zhao, Jiantao Huang, Shaoyong Yang, Tao Tang, Yaping Yang, Shengbao Aisimutuola, Patiguli Xu, Ruiqiang Hu, Jiahui Jia, Chunping Ma, Kai Li, Zhiqiang Jiang, Fangling Gao, Jie Lan, Haiyan Zhou, Yongfeng Zhang, Xinyan Huang, Sanwen Fei, Zhangjun Wang, Huan Li, Hongbo Yu, Qinghui |
author_sort | Li, Ning |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10181942 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group US |
record_format | MEDLINE/PubMed |
spelling | pubmed-101819422023-05-14 Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species Li, Ning He, Qiang Wang, Juan Wang, Baike Zhao, Jiantao Huang, Shaoyong Yang, Tao Tang, Yaping Yang, Shengbao Aisimutuola, Patiguli Xu, Ruiqiang Hu, Jiahui Jia, Chunping Ma, Kai Li, Zhiqiang Jiang, Fangling Gao, Jie Lan, Haiyan Zhou, Yongfeng Zhang, Xinyan Huang, Sanwen Fei, Zhangjun Wang, Huan Li, Hongbo Yu, Qinghui Nat Genet Article 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. Nature Publishing Group US 2023-04-06 2023 /pmc/articles/PMC10181942/ /pubmed/37024581 http://dx.doi.org/10.1038/s41588-023-01340-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Li, Ning He, Qiang Wang, Juan Wang, Baike Zhao, Jiantao Huang, Shaoyong Yang, Tao Tang, Yaping Yang, Shengbao Aisimutuola, Patiguli Xu, Ruiqiang Hu, Jiahui Jia, Chunping Ma, Kai Li, Zhiqiang Jiang, Fangling Gao, Jie Lan, Haiyan Zhou, Yongfeng Zhang, Xinyan Huang, Sanwen Fei, Zhangjun Wang, Huan Li, Hongbo Yu, Qinghui Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species |
title | Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species |
title_full | Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species |
title_fullStr | Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species |
title_full_unstemmed | Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species |
title_short | Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species |
title_sort | super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10181942/ https://www.ncbi.nlm.nih.gov/pubmed/37024581 http://dx.doi.org/10.1038/s41588-023-01340-y |
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