September 30, 2004

Tomato Seeds and All

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Over the next two years, Cornell researchers will join researchers around the world on a scientific endeavor to sequence the tomato genome. Ten other countries — including Germany, Belgium, the U.K. and Japan — will sequence eight of the 12 chromosomes found in a tomato, while the United States will tentatively sequence chromosomes one, two , five and 11.

Funded by the National Science Foundation, the project at Cornell will be led by three principal investigators — Prof. James Giovannoni, plant biology, Prof. Steven Tanksley, plant breeding and genetics, and researcher Lukas Mueller.

“The project is an opportunity to understand how genomes have evolved,” Giovannoni said. Scientists hope to use the sequenced genome as a reference for sequencing and decoding genomes of other closely related vegetables.

“We would like to have tomato as a reference sequence for the Solanaceae,” Mueller said. Many Solanaceae — an economically important family of plants that includes tomatoes, rice and potatoes — have already been sequenced, Mueller added.

But the sequencing of the tomato will provide a new source for comparison between already-sequenced Solanaceae, which will allow scientists to answer further questions about the functions of specific genes and how the plant genome has evolved in Solanaceae.

For example, tomatoes and other familiar plants such as coffee, potatoes and tobacco are “closely enough related that you can learn a lot [from gene sequencing] about the diversity in evolution that has brought about the different adaptations,” explained Giovannoni.

Possible answers to questions such as: “‘why does a tomato make a fleshy fruit while a potato grows underground?’ are the main excitement [of the project],” Giovannoni added.

The sequencing itself will be conducted on only parts of the tomato’s DNA, as there is strong evidence that only 25 percent of the genome contains actual genes.

“We believe the remaining 75 percent are mainly repetitive elements that don’t contain much important information,” Giovannoni said. Thus, determining which genome portions contain relevant genetic information will comprise the first portion of the project. Once that is completed, each portion will be sequenced and the collection of sequences will form a sort of library of DNA.

Afterward, “many different [computer] programs will be used to analyze what is in the [sequenced] genome,” explained Mueller. By comparing the DNA sequences to other known sequences, the computer programs are able to discover matches and similarities that will allow scientists to identify or associate new sequences with previously discovered ones.

When the sequences are first observed, “it is like reading a book where you can see the symbols but you cannot read the words — a bit like learning a foreign language,” Mueller said. However, as the programs point out recognizable sequences, scientists should be able to make some conclusions.

Mueller, who will be involved in the bioinformatics aspect of the project — the application of computer science to biology — will also lead an effort to standardize the way in which sequenced data is stored and presented.

“A big challenge, especially from the bioinformatics standpoint, is that everybody that sequences a chromosome does it in the same way, so that we don’t have 12 different things,” Mueller explained.

“We are trying to set some standards and guidelines.”

This project is the third NSF-funded project involving the tomato genome.

“The [first] project started about 6 years ago,” said Prof. Gregory Martin, plant pathology, a principal investigator on that project. “We sequenced about 1,800 genes [and] made [a] database, which we then distributed around the word … We were able to look at 8 to 10,000 genes at one time, and see how their expression might change due to something like pathogen.”

The second project involved a comparison between the tomato, potato and the pepper genome “to see what sort of gene sequences they shared,” Martin said. Scientists also employed a technique allowing them to “knock out” a gene and observe the effects of repressing that gene’s expression. For instance, when some genes were suppressed and a pathogen was introduced, the plant’s capability to defend against infection was altered or reduced.

“That tells you that that gene is playing a key role in the plant’s defense against pathogens,” Martin explained. The second project is ongoing for another two years.

Other findings of the first and second projects include a correlation between the how much light a tomato perceives it is receiving and the amount of beneficial nutritional compounds it produces.

The Boyce Thompson Institute, the USDA, and the University of Colorado will also assist in the tomato sequencing project.

Archived article by David Andrade
Sun Staff Writer