A Snapshot of the Emerging Tomato Genome Sequence

Abstract

The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high‐quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole‐genome shotgun techniques will be combined with the BAC‐by‐BAC approach to cover the entire tomato genome. The high‐quality reference euchromatic tomato sequence is expected to be near completion by 2010.

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

“…In this case, we relied heavily on the many genetic and genomics resources now available for tomato (Mueller et al 2009). But, we also took advantage of a publicly available EST database for coffee (Lin et al 2005).…”

“…Sufficiently detailed syntenic maps provide a means by which to access genomic information across species. For example, relative to coffee, many more genetic and genomic resources exist for tomato-the genome of which is currently being sequenced by an international consortium of scientists (Mueller et al 2009). The comparative maps provided here may allow coffee researchers to identify the orthologous counterparts in the tomato genome sequence.…”

“…The sequence of tomato chromosome 7 is currently being generated as part of the international initiative aimed at sequencing the entire tomato genome (M. Bouzayen personal communication, Mueller et al 2009). In the current study, we utilized 15.25 Mb of non-redundant sequences generated for chromosome 7.…”

Increase in Tomato Locule Number Is Controlled by Two Single-Nucleotide Polymorphisms Located NearWUSCHEL

“…New high-throughput sequencing tools allow genomes to be resequenced more quickly and cheaply. Because the tomato genome is now sequenced (http://solgenomics.net/genomes/ Solanum_lycopersicum/index.pl; Mueller et al, 2009), such an approach involving the comparison of a large number of full genomes could be used in the near future to identify an increasing number of genes for complex traits.…”

Genetic Transformation in Tomato: Novel Tools to Improve Fruit Quality and Pharmaceutical Production

“…This could allow inferring the sequence organization of other Solanaceae crops as basis for understanding how plants diversify and adapt to new and adverse environments. The recent release of the tomato genome sequence (Mueller et al, 2009), together with the powerful genetic and genomic resources available today for this species, allowed plant biotechnologists to implement novel methods to obtain new genotypes that could answer to new consumer, producer and processor requirements. These resources, in fact, could help the transfer of useful genes among species and/or improved genotypes through assisted breeding programs as well as through genetic transformation technologies.…”