Gene Discovery in the Cereals

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PI: W. Richard McCombie (Cold Spring Harbor Laboratory) Co PI: Doreen Ware (Cold Spring Harbor Laboratory)Key Collaborator: Robert A. Martienssen (Cold Spring Harbor Laboratory)Genomic sequence data holds the promise of dramatically advancing both the understanding of basic plant science, and of catalyzing practical advances in plant breeding. While the "complete", contiguous, "base perfect" sequence of a genome is the most useful outcome of a genome project, it is not necessary for most applications. Furthermore, base perfect sequence is prohibitive in terms of both time and cost for very large genomes or large numbers of moderately sized genomes. However, recent technological advances and soon-to-be broadly available technologies provide an attractive option for plant genomics. This project seeks to use next generation sequence technologies to identify the vast majority of genes in three closely related progenitor genomes of wheat (AA, AABB, and DD genome containing species) and hexaploid wheat (Chinese spring). Each genome will be sequenced to about 50x coverage with Illumina sequencers (paired end 100 base reads) and to about 8x-10x coverage using the Pacific Bio-Sciences sequencing technology. In addition, the project will sequence each genome with long range "strobe" reads on the Pacific Biosciences instrument that will amount to about 2 terabases of raw sequence. The sequences will be assembled and annotated for maximum use by the broader scientific community. All raw data, assemblies, and annotations will be released to the public as soon as they are generated and quality checked and prior to any publication that might be pursued. The broader impact of this project is to solve the data availability problem by providing about 2 terabases of raw genome sequence data to the broader cereal research community as well as the assemblies and annotation of the vast majority of genes in a large number of cereal genomes. It is expected that access to these data will radically accelerate functional genomics in wheat. All data generated in this project can be accessed through the project website, GenBank, and through the iPlant Collaborative (http://www.iplantcollaborative.org/). In addition, project updates will be coordinated with the International Wheat Genome Sequencing Consortium (IWGSC) and made available at (http://www.wheatgenome.org/Projects) and at GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml).