The tomato genome sequence provides insights into fleshy fruit evolution

TLDR

Tomato, a major crop and model for fruit development, belongs to the large Solanum genus that has undergone two genome triplications, enabling neofunctionalization of genes controlling fruit traits such as colour and fleshiness. The study reports a high‑quality genome sequence of domesticated tomato and a draft of its closest wild relative, Solanum pimpinellifolium, and compares them to each other and to the potato genome. The authors generated a high‑quality tomato genome assembly and a draft assembly of Solanum pimpinellifolium, then performed comparative genomics against each other and against Solanum tuberosum. The tomato genomes differ by only 0.6% and show recent admixture, whereas they diverge by over 8% from potato and contain multiple large inversions, and small RNAs in tomato and potato preferentially map to gene‑rich chromosomal regions.

Abstract

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 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.