PI: Jan Dvorak (University of California - Davis) CoPIs: Katrien M. Devos (University of Georgia), Olin D. Anderson and Ming-Cheng Luo (University of California - Davis)
Complete BAC-by-BAC sequencing of large plant genomes, such as those of wheat, barley, and other economically important plants, is currently prohibitively expensive. Next generation sequencing technologies, such as the 454 Life Sciences (Roche), Solexa (Illumina), and SOLiD (Applied BioSystems), offer sequencing with much higher throughputs and at greatly reduced costs. Unfortunately, the short read-lengths complicate the use of these techniques in de novo sequencing of eukaryotic genomes. That is particularly true for large plant genomes that contain vast amounts of repeated DNA sequences. The goal of this project is to assess a novel strategy for de novo sequencing with the SOLiD platform in collaboration with Applied BioSystems. This strategy will employ sequencing of two-dimensional pools of bacterial artificial chromosome (BAC) clones of genomic DNA. The strategy will be evaluated using two-dimensional pools of BAC clones of Aegilops tauschii, one of the diploid ancestors of polyploid wheat. A program will be written to deconvolute the pools and assemble sequences of individual clones.
Broader impacts: The development of a de novo sequencing strategy for the SOLiD sequencing platform will make it possible to seriously consider genome sequencing of species with large genomes, such as wheat, at realistic costs and in a realistic time frame. It is the hope that the sequencing technique and the software developed will be universally applicable to the sequencing of any large plant genome. The initial repository for public access to the assembly software developed is at http://wheatdb.ucdavis.edu:8080/wheatdb/index.jsp. The software will also be integrated with public web sites, such as GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml), that provides a compilation of molecular and phenotypic information on wheat and other cereals.
