Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

RICE SEQUENCE FINISHING: YEAR 3 - ATTACK OF THE CLONES

Arizona Genomics Insitute, The University of Arizona, Department of Plant Sciences, Tucson, AZ 85721

A high quality, high yield, low cost and simple method of DNA extraction has been established and used with the newly released Applied Biosystems 3730 Automated DNA Sequencers. This method has greatly decreased the time and cost in each stage of our production and finishing pipelines in our quest to completely sequence, finish and annotate the short arms of chromosomes 3 (over 16 Mb) and 10 (over 12 Mb). The finishing process consists of manual editing through the use of sequence analysis tools and alternative reaction chemistries. Raw sequence data is inspected for quality, discrepancies, coverage and a contiguity error rate less than 1 in 10,000 bases. The initial line of attack includes a pre-finishing step of correcting mis-assemblies and ordering contigs, adding public and private data, and completing two rounds of CONSED’s Autofinish reactions. Improving the process of high-throughput production, sharing techniques between sequencing centers, and utilizing advancements in technology, software, and chemistries are key elements in decreasing the complexities and time required to finish the rice genome. We will present our strategy and results for finishing BAC clones on the short arms of rice chromosomes 3 and 10.