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International Consortium Sequences Tomato Genome

NEW YORK (GenomeWeb News) – Members of the Tomato Genome Consortium reported today that they have sequenced the genomes of the domesticated tomato plant and its wild relative.

Using Sanger and second-generation sequencing technologies, the international team came up with a high-quality reference genome for domesticated tomato, Solanum lycopersicum, along with a draft version of the genome for S. pimpinellifolium, tomato's wild ancestor. They then compared the newly sequenced genomes to those of potato, a plant from the same genus, as well as other plants in an effort to find genes contributing to fruit features and more.

The findings, published online today in Nature, point to a pair of genome triplications in tomato's history. The first of these appears to have occurred in an ancient ancestor that is shared by plants in the Solanum lineage and by rosid plants such as grape and Arabidopsis, while a more recent genome triplication involved plants in the tomato and potato lineage.

By folding in gene expression, SNP, and other data, the researchers have already started finding clues about the genetic bases for important tomato traits — ranging from fruit flavor, color, and texture to smell and susceptibility to pathogens — as well as differences in gene use between tomato and potato plants.

"The genome sequences of tomato, S. pimpinellifolium, and potato provide a starting point for comparing gene family evolution and sub-functionalization in the Solanaceae [flowering plant family]," the study authors explained.

Along with being an important crop plant in its own right, valued at around $2 billion per year in the US, tomato serves as a useful model for understanding fruit development in other plants, the study authors explained.

Members of the consortium used Sanger and Roche 454 GS FLX Titanium sequencing to tackle the roughly 900 million base genome of a domestic tomato from the inbred Heinz 1706 cultivar, generating a high-quality, 760 million base genome assembly that spans 91 scaffolds on a dozen chromosomes.

Meanwhile, other participants in the tomato sequencing effort put together a 739 million base draft genome sequence for wild tomato, S. pimpinellifolium, by doing Illumina paired-end sequencing on DNA from the LA1589 cultivar.

To complement the genome sequencing side of the study, the team also did RNA sequencing on root, leaf, flower, and tomato fruit samples to gauge gene expression and small RNA levels during different stages of development in the domestic tomato plant. For the wild tomato counterpart, they sequenced RNAs from leaf and fruit samples taken at three stages of development.

Comparisons between the wild and domestic tomato genomes uncovered some 5.4 million SNPs between the genomes, which researchers estimate have diverged by around 0.6 percent.

More than 60 percent of the 31,760 domestic tomato genes from parts of the genome that were well-represented in the wild tomato draft sequence were either identical to one another or contained only synonymous mutations. The other 40 percent or so contained differences expected to affect the function of resulting proteins.

Meanwhile, the team's comparison between tomato and potato, another plant in the Solanum genus, revealed almost 9 percent nucleotide divergence across euchromatin regions in the species. That divergence jumped to more than 30 percent over parts of the genome that were heavy in intergenic sequences or repeat rich heterochromatin, apparently owing to diversity in these regions in the potato genome.

From the nearly 35,000 protein-coding genes predicted in the tomato genome, researchers narrowed in on 8,615 that are shared between tomato, potato, Arabidopsis, rice, and grape plants. Another 727 were specific to the fleshy-fruited plants, tomato, potato, and grape, they noted.

When they focused in on the more than 18,300 orthologous genes shared by tomato and potato, the researchers tracked down nearly 140 genes showing signs of diversifying selection and 147 containing signals associated with purifying selection.

Along with their overall analyses of past genome duplication and triplication events in plants, the researchers used gene expression and other information to look at how the events may have influenced the advent of genes involved in fruit development.

With the tomato genome in hand, the study authors added, it will also be possible to re-sequence other tomato varieties and do other follow-up studies to help decipher and apply the plant's genetic information.

"Now we can start asking a lot more interesting questions about fruit biology, disease resistance, root development and nutritional qualities," James Giovannoni, a researcher with Cornell University's Boyce Thompson Institute for Plant Research and the US Department of Agriculture, explained in a statement.

"Tomato genetics underlies the potential for improved taste every home gardener knows and every supermarket shopper desires," added Giovannoni, one of the principal investigators on the project, "and the genome sequence will help solve this and many other issues in tomato production and quality."

Information generated through the tomato sequencing effort is available online through a web site that houses information on tomato, potato, pepper, coffee, and other plants.