NC State University Maps Tobacco Genome

North Carolina State University scientists have completed a nearly five-year, $17.6 million effort to map the genome of tobacco.

With completion of the Tobacco Genome Initiative, which was funded by Philip Morris USA, the genetic information that makes a tobacco plant a tobacco plant will be made available to the public, said Dr. Charles Opperman, plant pathology professor and co-director of the project. Dr. Steven Lommel, interim associate dean for research for the NC State College of Agriculture and Life Sciences and university assistant vice chancellor for research, also directed the effort.

Opperman said the genetic information will be available online through the National Institutes of Health National Center for Biotechnology Information GenBank Web site, http://www.ncbi.nlm.nih.gov/Genbank/index.html, and on an NC State University Web site, http://www.tobaccogenome.org/.

The genome of an organism is the genetic blueprint for that organism. The genomes of all living things are made up of DNA, which in turn is composed of molecules called bases or nucleotides. The sequence in which these bases – which are identified by the letters A, G, T, C – appear determines the identity of an organism. The genomes of an oak tree and a black bear are both made up of the same four bases. It is the order, or sequence, in which the bases appear that distinguishes an oak tree from a black bear.

Scientists in the College of Agriculture and Life Sciences at NC State determined the nucleotide sequence of the gene space of tobacco, the part of the tobacco genome that contains genes and genetic coding that controls genes. Opperman said the tobacco genome contains approximately 4.5 billion bases, which is 1.5 times the size of the human genome; however, only 20 to 25 percent of a tobacco plant’s genome is considered gene space.

The gene space of a tobacco variety called Hicks was sequenced. Hicks is a variety of broadleaf, flue-cured tobacco, and it was suggested for the project by NC State tobacco breeders and Philip Morris USA because it has been used in breeding widely grown tobacco varieties.

Opperman said that the Tobacco Genome Initiative identified sections, or regions, of the sequence that are likely to be genes. He estimated the project identified greater than 95 percent of tobacco’s genes.

While the project identified portions of the tobacco genome thought to be genes, it did not necessarily determine what the genes do.

“We can probably assign identity to about half the genes,” Opperman said. “And we can speculate on what they do.”

He added, “A good example is resistance genes.” These are genes that help the tobacco plant survive, or resist, a disease, pest or other assault. “We can identify lots of things that look like resistance genes, but don’t know what they do. That’s for other people to figure out.”

Opperman estimated that tobacco has about 36,000 genes.

Tobacco is widely used as a model for a range of plant studies, Lommel pointed out, so the information provided by the project should provide valuable insight to plant scientists working with plants other than tobacco. The information provided by the project will aid scientists studying how other plant species develop, yield and resist pests and pathogens.

Tobacco’s genetic blueprint should be particularly useful in studies of crops such as tomatoes, potatoes and peppers, which, like tobacco, are solanaceous plants and are similar genetically.

Tobacco becomes one of a handful of plants whose gene catalog has been sequenced. The genome of rice has been sequenced, as have the genomes of Arabidopsis, Medicago truncatula and Lotus Japonicus, all of which are used as models in scientific studies. Sequencing of a range of other plants, including corn, soybean, tomato and potato is underway.

Opperman said Orion Genomics, a St. Louis, Mo., company, played a key role in the project. NC State contracted with Orion for use of the company’s proprietary Gene Thresher technology, which identifies gene-rich regions of a genome.

“Orion was a great partner,” Opperman said.