Plant & Animal Genome IX Conference

Poster: Sequencing & EST
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THE TIGR RICE GENOME PROJECT: SEQUENCE AND TOOLS FOR RICE BIOLOGISTS

The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850 USA

TIGR is participating in the International Rice Genome Sequencing Project and has been assigned chromosomes 3 and 10. We are collaborating with Clemson University/Cold Spring Harbor Laboratory/Washington University and the Plant Genome Initiative at Rutgers to complete these chromosomes. We are using a BAC shotgun sequencing to complete our regions of chromosomes 3 and 10. As of October 2000, we have over 12 Mb of rice genomic DNA in our high throughput sequencing pipeline at TIGR (http://www.tigr.org/tdb/rice). All of the TIGR rice sequences are annotated for gene content. All sequence and annotation data are released to Genbank/DDBJ/EMBL and displayed on the TIGR Rice Web Site (www.tigr.org/tdb/rice). We have developed a new version of the gene prediction program, GLIMMER, that has been trained for use with rice sequences. We are also experimentally validating the accuracy of all gene prediction programs available for rice. In addition to our sequencing and annotation efforts, we perform other informatic analyses of rice genomic DNA. These include 1) in silico anchoring of BAC clones to the genetic map using alignments of the available BAC end sequences with available genetic markers, 2) monitoring the progress of the IRGSP where we search all completed and in progress BAC/PACs against all available rice markers, 3) identification of putative orthologues and paralogues of rice sequences, and 4) global alignments of rice genome sequences with all available plant transcripts. An update of our progress and analyses will be presented. As with all other TIGR Rice information, these data can be accessed on the TIGR Rice web site at www.tigr.org/tdb/rice.