The tomato genome has tripled several times in a row about 60 million years ago, which would have been able to survive ice ages, as recorded an international research that has involved several Spanish research centers to reach the aim of sequence its genome. "The duplications could have saved the tomato in the last great massive extinction" that wiped out 75% of world's species, including dinosaurs, says the researcher of the Institute of Molecular and Cellular Biology of Plants Primo Yúfera (joint center CSIC and the Valencia University) Antonio Granell, who has led the Spanish part of the job.
Scientists have completed the genome sequencing of the tomato crop (Solanum lycopersicum) and its wild relative (Solanum pimpinellifolium) and have compared it with several closely related species such as grapes and potatoes. It is estimated that the first time the genome of this vegetable tripled was before tomatoes and grapes had taken different evolutionary paths and the second, more recently, was before the tomatoes and potatoes separated, according to the study published in the journal Nature.
Genome duplications "are a mechanism for generating new features," says Granell. "If you want to create a saw from a scissor, you can alter the scissors to look like a saw, but you'll run out the scissors. To avoid this loss what nature does is double the scissors and apply changes to one copy, so they don't miss the original structure in the event that such change would not benefit the species," explains.
Over time, the repeated genetic content which becomes obsolete because of the new features, gradually is remodeled. In the case of tomato, for example, some genes related to their texture and color are produced by this replication and specialization process.
In this project, which has seen eight years of work, 300 researchers have taken part from study centers in 14 countries, among which is Spain, as well as Germany, Argentina, Belgium, China, South Korea, France, Holland, India, Israel, Italy, Japan, UK and USA. Specifically, there were involved the Barcelona Supercomputing Center - National Supercomputing Center (BSC-CNS), the Institute for Biomedical Research (IRB), the National Center for Genome Analysis (CNAG), the National Bioinformatics Institute, the Center for Genomic Regulation (CRG), the Institute of Molecular and Cellular Biology of Plants and the Institute of Subtropical Horticulture and Mediterranean La Mayora (joint CSIC and the University of Malaga, and businesses Genome Bioinformatics and Genome Systems). Spanish participation focused on sequencing of chromosome 9 and the introduction of new sequencing technologies.
The study concludes that the changes that happened millions of years ago contributed to the emergence of new species of fruit plants and its diversification. Tomatoes belong to the family Solanaceae, which includes potatoes, peppers, eggplants, and even ornamental and medicinal plants such as petunia, tobacco, belladonna or mandrake, present in different parts of the world.
Genetic differences between the tomato and potato are higher than 8%, while between the tomato crop and the wild one the difference is only 0.6%. This means that there are only six changes per 1,000 nucleotides, indicating that the two species diverged 1.3 million years ago.
Sequencing the genome, scientists have created the molecular basis to being able to study the tomato and to investigate new ways of cultivation that allows us to generate strategies to help this species to resist pests and lack of water.
"The genome researchers are a way to understand the evolution of higher plants and, in the future, they will offer new tools for agriculture," explains researcher of the Center for Genomic Regulation (CRG) Francisco Chamber. In fact, we now know that some repeated fragments include genes that would be responsible for some properties of the tomato, as the formation of a tougher skin to enhance the fruit protection. "Tomato is one of the most common crop plants and with greater exploitation", so it has a great interest.
About 35,000 genes
The tomato DNA has about 35,000 genes expressed along about 900 million pairs bases. Among its various chains of adenine, guanine, cytosine and thymine, this vegetable has the signs of having undergone several duplications.
"The gene identification is the first step to convert the genome sequence of a species in relevant information from the biological point of view," says Roderic Guigó of Bioinformatics and Genomics Laboratory of CRG. The contribution of his laboratory in this study involved the development of software for gene detection.
The project was carried out by an international consortium and aims to offer the tomato genome to public and private research groupsto improve the understanding of the biology of this plant, essential in agriculture. Previous versions of the sequence have been available for over a year on a public accessible website. Granell meanwhile headlined the importance of "spreading such developments as soon as possible, especially when it comes to public inquiries, so that they can return to society the benefits soon."
The sequence of tomato and related resources are accessible and http://mips.helmholtz-muenchen.de/plant/tomato/index.jsp http://solgenomics.net.
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