Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

The Tobacco Genome Initiative: A Gene Discovery Platform

Charles H Opperman¹ , Steven A Lommel¹ , Mark Burke¹ , Joanna Carlson¹ , Carol George¹ , Sandy Gove¹ , T.D. Houfek¹ , Stuart Jefferys¹ , Sam Kalat¹ , Ron, Jr. King¹ , Jennifer Levin¹ , P.C. Little¹ , Amy Lumpkin¹ , T. Ross¹ , Aimee Salstead¹ , Elizabeth Scholl¹ , Bryon Sosinski¹ , P.J. Stevens¹ , Scott Zekanis¹ , J. Frelinger¹ , Nate Lakey² , Joey Bidell² , Arief Budiman² , Alec Hayes³

¹  College of Agriculture and Life Sciences, NC State University, Raleigh, NC 27695

²  Orion Genomics, LLC, St Louis, MO, 63108

³  Philip Morris USA, Research Center, Richmond, VA 23261, USA

Although cultivated tobacco, Nicotiana tabacum, is of great economic significance, relatively little information exists on its genome structure and organization. N. tabacum has a very large genome size compared with other cultivated solanaceous plants. At approximately 4.5 billion base pairs, it is 1.5 times the size of the human genome. As with the human genome, the vast majority of these base pairs occurs as highly repetitive non-coding sequence. We are employing a combination of strategies to identify a large percentage of genes in N. tabacum. We are employing a methyl filtration library approach to identify gene-rich regions in N. tabacum in order to expedite the gene discovery. To date, we have sequenced 305,280 lanes of a methyl filtered library and observe a nearly 10-fold increase in gene discovery in filtered vs. non-filtered libraries. In addition, we constructed a BAC library (9.7-fold genome coverage) and initiated BAC-end sequencing as part of our physical mapping program. We have fingerprinted 45,331 BAC clones using the four dye protocol and have sequenced 18 BAC clones to ~5X coverage. We have also performed EST sequencing from various Nicotiana libraries and, to date, have sequenced 73,344 ESTs. Results from these experiments will be discussed, as well as overall gene discovery rates and genome organization. The utility of a whole genome approach to gene discovery will be examined.