The tomato genome sequence provides insights into fleshy fruit evolution

S. Sato, S. Tabata, H. Hirakawa, R.M. Klein Lankhorst, H. de Jong, R.C.H.J. van Ham, E. Datema, S. Smit, E.G.W.M. Schijlen, J.C. van Haarst, S.A. Peters, M.H.C. Henkens, M.J. van Staveren, P.J.W. Mooijman, T. Hesselink, J. van de Belt, D. Szinay, Y. Bai, R.G.F. Visser

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 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 pimpinellifolium2, 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.
Original languageEnglish
Pages (from-to)635-641
JournalNature
Volume485
DOIs
Publication statusPublished - 2012

Fingerprint

Solanum
tomatoes
fruits
genome
potatoes
genes
wild relatives
Solanum lycopersicum
Solanum tuberosum
fruiting
Angiospermae
nucleotides
promoter regions
Arabidopsis
RNA
soybeans
color
crops
habitats

Keywords

  • lycopersicon-esculentum
  • gene
  • diversification
  • arabidopsis
  • patterns
  • ortholog
  • history
  • sorghum
  • potato

Cite this

Sato, S. ; Tabata, S. ; Hirakawa, H. ; Klein Lankhorst, R.M. ; de Jong, H. ; van Ham, R.C.H.J. ; Datema, E. ; Smit, S. ; Schijlen, E.G.W.M. ; van Haarst, J.C. ; Peters, S.A. ; Henkens, M.H.C. ; van Staveren, M.J. ; Mooijman, P.J.W. ; Hesselink, T. ; van de Belt, J. ; Szinay, D. ; Bai, Y. ; Visser, R.G.F. / The tomato genome sequence provides insights into fleshy fruit evolution. In: Nature. 2012 ; Vol. 485. pp. 635-641.
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abstract = "Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 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 pimpinellifolium2, 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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author = "S. Sato and S. Tabata and H. Hirakawa and {Klein Lankhorst}, R.M. and {de Jong}, H. and {van Ham}, R.C.H.J. and E. Datema and S. Smit and E.G.W.M. Schijlen and {van Haarst}, J.C. and S.A. Peters and M.H.C. Henkens and {van Staveren}, M.J. and P.J.W. Mooijman and T. Hesselink and {van de Belt}, J. and D. Szinay and Y. Bai and R.G.F. Visser",
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The tomato genome sequence provides insights into fleshy fruit evolution. / Sato, S.; Tabata, S.; Hirakawa, H.; Klein Lankhorst, R.M.; de Jong, H.; van Ham, R.C.H.J.; Datema, E.; Smit, S.; Schijlen, E.G.W.M.; van Haarst, J.C.; Peters, S.A.; Henkens, M.H.C.; van Staveren, M.J.; Mooijman, P.J.W.; Hesselink, T.; van de Belt, J.; Szinay, D.; Bai, Y.; Visser, R.G.F.

In: Nature, Vol. 485, 2012, p. 635-641.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Sato, S.

AU - Tabata, S.

AU - Hirakawa, H.

AU - Klein Lankhorst, R.M.

AU - de Jong, H.

AU - van Ham, R.C.H.J.

AU - Datema, E.

AU - Smit, S.

AU - Schijlen, E.G.W.M.

AU - van Haarst, J.C.

AU - Peters, S.A.

AU - Henkens, M.H.C.

AU - van Staveren, M.J.

AU - Mooijman, P.J.W.

AU - Hesselink, T.

AU - van de Belt, J.

AU - Szinay, D.

AU - Bai, Y.

AU - Visser, R.G.F.

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N2 - Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 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 pimpinellifolium2, 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.

AB - Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 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 pimpinellifolium2, 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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KW - sorghum

KW - potato

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