The tomato genome sequence provides insights into fleshy fruit evolution

• Published in: Nature (London) Vol. 485; no. 7400; pp. 635 - 641
• Main Authors: Tomato Genome Consortium, Sato, S, Guigó Serra, Roderic, Cámara, Francisco, Gianese, S
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 31.05.2012; Nature Publishing Group
• Subjects: 631/136; 631/208/212/2304; 631/449/2491; 631/449/2679/2684; Arabidopsis - genetics; Artificial chromosomes; Binding sites; DNA sequencing; Evolution; Evolution, Molecular; Fruit; Fruits; Genes; Genetic aspects; Genetic diversity; Genetic Variation - genetics; Genome, Plant - genetics; Genomes; Genomics; Genètica evolutiva; Genètica molecular; Genòmica; Glycine max - genetics; Governmental accounting; Humanities and Social Sciences; letter; Life Sciences; Molecular Sequence Data; multidisciplinary; Nucleotide sequencing; Phylogeny; Physiological aspects; Pipelines; Plant genetics; Plants; Potatoes; RNA, Plant - genetics; Science; Science (multidisciplinary); Sequence Analysis, DNA; Solanum lycopersicum - genetics; Solanum lycopersicum - physiology; Solanum tuberosum - genetics; Soybeans; Synteny; Tomatoes; Tomàquets; Vegetal Biology; Lycopersicon-esculentum ; gene ; diversification : arabidopsis ; patterns ; ortholog ; history ; sorghum ; potato
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/nature11119

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum . 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.