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

The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

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SummaryAnthocyanin biosynthesis in flowers of Petunia hybrida is controlled by the regulatory genes an1, an2 and an11. Seven classes of cDNA clones homologous to transcripts that are down-regulated in an1-, an2-and an11-mutants were isolated via differential cDNA cloning. Genetic mapping, antisense RNA experiments and analyses of mutant alleles demonstrated that one class of clones originated from the Rt locus. The rt gene has no introns and encodes a protein with homology to mammalian glucuronosyl transferases and flavonoid 3-O-glucosyltransferase (UF3GT) encoded by the bzl gene from Zea mays. As the Rt locus controls the rhamnosylation of reddish anthocyanin-3-O-glucosides which is the first in a series of modifications that finally yield magenta or blue/purple coloured anthocyanins, this suggests that rt encodes an anthocyanin rhamnosyl transferase. Molecular analysis of two mutant rt alleles showed that their expression is blocked by different DNA insertion elements. Mutability of the rt-vu15 allele results from the presence of a 284 bp transposable element (dTphl) in the rt promoter region, causing a block in transcription. The protein coding region of the rt.r27 allele contains a 442 bp insertion (dTph3) resulting in premature polyadenylation of rt transcripts. Although dTph3 cannot transpose, it has sequence characteristics of transposable elements, suggesting that it is a defective member of a new family of transposable elements.