The tomato genome sequence provides insights into fleshy fruit evolution

Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu, Kenta Shirasawa, Sachiko Isobe, Takakazu Kaneko, Yasukazu Nakamura, Daisuke Shibata, Koh Aoki, Michael Egholm, James Knight, Robert Bogden, Changbao Li, Yang Shuang, Xun Xu, Shengkai Pan, Shifeng Cheng, Xin Liu, Yuanyuan RenJun Wang, Alessandro Albiero, Francesca Dal Pero, Sara Todesco, Joyce Van Eck, Robert M. Buels, Aureliano Bombarely, Joseph R. Gosselin, Minyun Huang, Jonathan A. Leto, Naama Menda, Susan Strickler, Linyong Mao, Shan Gao, Isaak Y. Tecle, Thomas York, Yi Zheng, Julia T. Vrebalov, JeMin Lee, Silin Zhong, Lukas A. Mueller, Willem J. Stiekema, Paolo Ribeca, Tyler Alioto, Wencai Yang, Sanwen Huang, Yongchen Du, Zhonghua Zhang, Glenn Bryan, Andrew H. Paterson, Tomato Genome Consortium

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    1692 Citations (Scopus)

    Abstract

    Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.</p>
    Original languageEnglish
    Pages (from-to)635-641
    Number of pages7
    JournalNature
    Volume485
    Issue number7400
    DOIs
    Publication statusPublished - 31 May 2012

    Cite this

    Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata, D., Aoki, K., Egholm, M., Knight, J., Bogden, R., Li, C., Shuang, Y., Xu, X., Pan, S., Cheng, S., Liu, X., ... Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635-641. https://doi.org/10.1038/nature11119