Journal
NATURE
Volume 485, Issue 7400, Pages 635-641Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nature11119
Keywords
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Categories
Funding
- Argentina: INTA
- Argentina: CONICET
- Belgium: Flemish Institute for Biotechnology
- Belgium: Ghent University
- China: The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
- Ministry of Science and Technology [2006AA10A116, 2004CB720405, 2006CB101907, 2007DFB30080]
- Ministry of Agriculture [2007-Z5]
- National Natural Science Foundation [36171319]
- Postdoctoral Science Foundation [20070420446]
- European Union [EU-SOL PL 016214]
- France: Institute National de la Recherche Agronomique
- France: Agence Nationale de la Recherche
- Germany: the Max Planck Society
- India: Department of Biotechnology, Government of India
- Indian Council of Agricultural Research
- Italy: Ministry of Research
- Ministry of Agriculture
- FILAS foundation
- ENEA
- CNR-ENEA [L. 191/2009]
- Japan: Kazusa DNA Research Institute Foundation
- Japan: National Institute of Vegetable and Tea Science
- Korea: KRIBB
- Korea: Crop Functional Genomics Research Center (CFGC), MEST
- Netherlands: Centre for BioSystemsGenomics, Netherlands Organization for Scientific Research
- Spain: Fundacion Genoma Espana
- Cajamar
- FEPEX
- Fundacion Seneca
- ICIA
- IFAPA
- Fundacion Manrique de Lara
- Instituto Nacional de Bioinformatica
- UK: BBSRC [BB/C509731/1]
- DEFRA
- SEERAD
- USA: NSF [DBI-0116076, DBI-0421634, DBI-0606595, IOS-0923312, DBI-0820612, DBI-0605659, DEB-0316614, DBI 0849896, MCB 1021718]
- USDA [2007-02773, 2007-35300-19739]
- USDA-ARS
- NSF
- ICREA Funding Source: Custom
- BBSRC [BBS/E/T/000PR6193, BB/G02491X/1, BB/G006199/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/C509731/1, BB/G02491X/1, BB/G006199/1, BBS/E/T/000PR6193] Funding Source: researchfish
- Grants-in-Aid for Scientific Research [24113518] Funding Source: KAKEN
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [820612] Funding Source: National Science Foundation
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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.
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