The tomato genome sequence provides insights into fleshy fruit evolution

Nature. 2012 May 30;485(7400):635-41. doi: 10.1038/nature11119.


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

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Evolution, Molecular*
  • Genetic Variation / genetics
  • Genome, Plant / genetics*
  • Genomics
  • Glycine max / genetics
  • Molecular Sequence Data
  • Phylogeny
  • RNA, Plant / genetics
  • Sequence Analysis, DNA
  • Solanum lycopersicum / genetics*
  • Solanum lycopersicum / physiology
  • Solanum tuberosum / genetics
  • Synteny


  • RNA, Plant

Associated data

  • GENBANK/CM001064
  • GENBANK/CM001065
  • GENBANK/CM001066
  • GENBANK/CM001067
  • GENBANK/CM001068
  • GENBANK/CM001069
  • GENBANK/CM001070
  • GENBANK/CM001071
  • GENBANK/CM001072
  • GENBANK/CM001073
  • GENBANK/CM001074
  • GENBANK/CM001075
  • GEO/GSE33507