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

We have screened a large tomato EST database against the Arabidopsis genomic sequence and report here the identification of a set of 1025 genes (referred to as a conserved ortholog set, or COS markers) that are single or low copy in both genomes (as determined by computational screens and DNA gel blot hybridization) and that have remained relatively stable in sequence since the early radiation of dicotyledonous plants. These genes were annotated, and a large portion could be assigned to putative functional categories associated with basic metabolic processes, such as energy-generating processes and the biosynthesis and degradation of cellular building blocks. We further demonstrate, through computational screens (e.g., against a Medicago truncatula database) and direct hybridization on genomic DNA of diverse plant species, that these COS markers also are conserved in the genomes of other plant families. Finally, we show that this gene set can be used for comparative mapping studies between highly divergent genomes such as those of tomato and Arabidopsis. This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution.

We report herein the mapping of 115 PCR-based orthologous markers, including 110 conserved ortholog set or COSII markers, on the reference RFLP map of eggplant. The result permitted inference of a detailed syntenic relationship between the eggplant and tomato genomes. Further, the position of additional 522 COSII markers was inferred in the eggplant map via eggplant-tomato synteny, bringing the total number of markers in the eggplant genome to 869. Since divergence from their last common ancestor approximately 12 million years ago, the eggplant and tomato genomes have become differentiated by a minimum number of 24 inversions and 5 chromosomal translocations, as well as a number of single gene transpositions possibly triggered by transposable elements. Nevertheless, the two genomes share 37 conserved syntenic segments (CSSs) within which gene/marker order is well preserved. The high-resolution COSII synteny map described herein provides a platform for cross-reference of genetic and genomic information (including the tomato genome sequence) between eggplant and tomato and therefore will facilitate both applied and basic research in eggplant.

We report herein the development of a pepper genetic linkage map which comprises 299 orthologous markers between the pepper and tomato genomes (including 263 conserved ortholog set II or COSII markers). The expected position of additional 288 COSII markers was inferred in the pepper map via pepper-tomato synteny, bringing the total orthologous markers in the pepper genome to 587. While pepper maps have been previously reported, this is the first complete map in the sense that all markers could be placed in 12 linkage groups corresponding to the 12 chromosomes. The map presented herein is relevant to the genomes of cultivated C. annuum and wild C. annuum (as well as related Capsicum species) which differ by a reciprocal chromosome translocation. This map is also unique in that it is largely based on COSII markers, which permits the inference of a detailed syntenic relationship between the pepper and tomato genomes-shedding new light on chromosome evolution in the Solanaceae. Since divergence from their last common ancestor is approximately 20 million years ago, the two genomes have become differentiated by a minimum number of 19 inversions and 6 chromosome translocations, as well as numerous putative single gene transpositions. Nevertheless, the two genomes share 35 conserved syntenic segments (CSSs) within which gene/marker order is well preserved. The high resolution COSII synteny map described herein provides a platform for cross-reference of genetic and genomic information (including the tomato genome sequence) between pepper and tomato and therefore will facilitate both applied and basic research in pepper.

We report the isolation and characterization of seven nuclear genes encoding polyphenol oxidase (PPO) in tomato (Lycopersicon esculentum cv. VFNT Cherry). The seven genes (PPOs A, A', B, C, D, E and F) fall into three structural classes (I, II, and III) based on Eco RI and Hind III restriction fragment length polymorphisms (RFLP). RFLP mapping and PFGE analysis demonstrated that the genes reside on chromosome 8, and may be clustered within a 165 kb region. Phage insert mapping demonstrated PPO E and PPO F (both class III), and PPOs B, D and A (classes I, II and I respectively) are grouped within separate 12.4 kb clusters. The complete nucleotide sequence was determined for each gene. Comparison to cDNAs revealed that the PPOs lack introns. A transcript of about 2 kb is expected for each PPO. Each PPO possesses a region encoding a transit peptide characteristic of polypeptides targeted to the thylakoid lumen. Predicted precursor polypeptides range in mass from 66 to 71 kDa and predicted mature polypeptides range from 57 to 62 kDa. All the PPOs encode two putative copper-binding sites characteristic of bacterial, fungal and mammalian tyrosinases. Five of the seven PPOs possess divergent DNA sequences in their 5' promoter regions. These flanking sequence differences may regulate the differential expression of PPO genes.