IC4R002-Genome-2002-11935018

Project Title

• A Draft Sequence of the Rice Genome (Oryza sativa L. ssp.japonica)

The Background of This Project

• The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.

Research Findings

• Translated HMLgenes300 were classified with the software package INTERPRO (27,28). INTERPRO output was filtered to create sets of the longest protein domain for each associated protein, and domains were categorized using Gene Ontology (GO) software(29). The results of these classifications are shown in Fig. 1; about 44% of Hgenes, 32% of Mgenes, and 5% of Lgenes were classified, respectively. Most of the classified proteins fall into the categories of metabolism and cell communication/signal transduction.

Fig. 1. Rice gene prediction classifications. HMLgenes300 were classified with Interpro and GO software (27–29); the categories generated are shown.

• Eighty-five percent of Arabidopsis predicted proteins (21,590 of 25,554) were significantly homologous to HMLgenes300 predicted proteins; of these, 2565 show very strong conservation between Arabidopsis and rice (Fig. 2).

Fig. 2. Similarity of 25,554 Arabidopsis proteins and best rice homologs. Predicted Arabidopsis proteins (October 2001, ftp.tigr.org) were compared (BLASTP E value # –6) with HMLgenes300 translations.The expectation values range from E , 2180(high homology) to E . 26 (low homology) and are depicted in intervals spanning 10 exponents(e.g., , 2180, 2180 to 2171, 2170 to 2161, etc.)

Labs working on this Project

• Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA (www.tmri.org).
• Bryan College, Dayton, TN 37321, USA.
• Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA.
• Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
• Clemson University Genomics Institute, 100 Jordan Hall, Clemson, SC 29630, USA.
• Myriad Genetics, 320 Wakara Way, Salt Lake City,UT 84108, USA.

Corresponding Author

• stephen.goff@syngenta.com