¹ Clemson University Genomics Institute, Clemson, SC 29634. USA

² Cold Spring Horbor Lita Annenberg Hazen Genome Sequencing Center, Cold Spring Harbor, NY 11724. USA

³ Washington University Genome Sequencing Center, St. Louis, MO 63108. USA

The objectives of the CCW Rice Genome Sequencing Consortium, funded in October 1999¹, are to sequence and annotate the short arms of rice chromosomes 10 and 3. As a prelude rice genome sequencing, CUGI has focused on the development of a sequence tagged connector (STC)/BAC fingerprint framework to facilitate the International Rice Genome Sequencing Project (IRGSP). The framework consists of 4 elements: 1) two deep-coverage large insert BAC libraries (HindIII and EcoRI)²; 2) a STC database³; 3) a Fingerprint database³ and 4) a Genome Anchoring database. 1. The Hind III BAC library contains 36,874 clones with an average insert size of 130 kb and the EcoR1 library contains 55,296 cones with average insert size of 120 kb. Combined, the BAC libraries cover approximately 26 genome equivalents. 2. The STC-DB is composed of DNA sequence derived from the ends of the DNA inserts in the HindIII and EcoRI BAC libraries. Sequencing was completed in April 2000 and resulted in the generation of 63,432 and 47,006 end sequences from the HindIII and EcoRI libraries respectively, and comprise over 36 Mb of high-quality rice genomic sequence deposited in Genbank. 3. The Fingerprint DB contains 63,233 high-resolution HindIII fingerprints derived from both BAC libraries. BAC clones were fingerprinted in duplicate on 1% agarose gels and assembled into contigs using FPC (FingerPrinted Contigs: Soderlund et al. 2000). At a cut off of 1 X 10^-12, the 63,233 clones assembled into 1038 contigs and 2927 singletons. 4. The Genome Anchoring DB contains hybridization data (wet lab and in silico) to the BAC libraries and STC and FP databases. Currently 706 markers (RFLPs and Overgos derived from STCs) have been placed on the physical map thereby anchoring 268 of the 454 BAC contigs (59%). We estimate the 268 contigs cover about 323 Mb of the rice genome. Using this framework, CCW has validated and sequenced 146 BAC clones from chr 3 and 10 (about 20 Mb of draft sequence). Data will be presented describing the Framework Project, CCW's sequencing progress to date, and early applications of our sequencing efforts to better understand and sequence the rice genome. Funded by: ¹ USDA/NSF/DOE Rice Genome Sequencing Program, ² Rockefeller Foundation, ³ Novartis