Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Exploring The Pine Genome Using Cot Filtration And 454 Life Sciences Massively Parallel Shotgun Sequencing

Daniel G. Peterson^1,2 , Philippe Chouvarine^1,2 , Supaphan Thummasuwan^1,2 , Surya Saha^1,3 , Dipaloke Mukherjee^1,2 , John E. Carlson⁴

¹  Mississippi Genome Exploration Laboratory, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA

²  Department of Plant and Soil Sciences, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA

³  Department of Computer Science and Engineering, 300 Butler Hall, Mississippi State University, Mississippi State, MS, 39762, USA

⁴  Schatz Center for Tree Molecular Genetics, School of Forest Resources and Huck Institutes for Life Sciences, The Pennsylvania State University, 405C Life Sciences Building, University Park, PA, 16802, USA

The 454 Life Sciences (www.454.com) Genome Sequencer 20 (GS20) is a new, massively parallel pyrosequencing apparatus with a sequencing capacity 100 times greater than that of the most advanced Sanger/capillary-based system. Consequently, the GS20 offers small research groups the power to affordably conduct high-throughput sequencing projects previously limited to large sequencing centers. Here we present preliminary research on the utility of the GS20 in characterizing genomic DNA and Cot-filtered gene- and repeat-enriched fractions from loblolly pine, Pinus taeda, L., the most economically important tree in the U.S. Additionally, we compare and contrast pine sequence data obtained using the GS20 with Cot-based cloning and sequencing data generated via standard Sanger/capillary methods. Initial results suggest that the combination of Cot filtration and GS20 sequencing will afford considerable insight into the enormous pine genome (1C = 21,658 Mb) and will facilitate comparative genomics in gymnosperms and other large genome species.

This work is funded, in part, by NSF DBI-0421717. Additional information is available at www.mgel.msstate.edu.