Characterization of Rice Genomes and Transcriptomes Using Novel Sequencing Technologies

Cold Spring Harbor Laboratory, Cold Spg Hbr NY

Investigators

Abstract

PI: W. Richard McCombie (Cold Spring Harbor Lab) CO-PIs: Li Liao (University of Delaware), Black C. Meyers (University of Delaware) DNA sequencing technology has entered a phase of very rapid change after nearly a decade of slower, incremental changes. In particular, radically different types of sequencers ( e.g. 454 Lifesciences, Solexa) have been developed which have provided large amounts of data but much shorter individual sequence lengths than are provided by current sequencers. The primary goal of this proposal is to (1) test these methods by genomic sequencing of orthologous regions from four rice species (Oryza glaberrima, O. punctata, O. officinalis, and O. minuta) (2) develop new strategies and software tools to most effectively use these new sequencers in combination with previous sequencers. During development and testing of the assembly algorithm, the investigators will assess the assembly of different ratios (mixtures) of coverage from each technology platform. As a result of this project, the investigators will determine the most efficient method to sequence additional important plant genomes in the future using one or a combination of these sequencing technologies. Access to project outcomes Sequence data will be incorporated into Gramene (www.gramene.org) and the Oryza Map Alignment Project (www.omap.org). Software will be accessible via http://www.cis.udel.edu/~lliao/.