Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species

Rice (Oryza sativa) is a model species for monocotyledonous plants, especia lly for membvis in the grass family. Several attributes such as small genom e size, diploid nature, transformability, and establishment of genetic and molecular resourses make it a tractable organism for plant biologists. With an estimated genome size of 430 Mb (Arumuganathan and Earle, 1991), it is feasible to obtain the complete genome sequence of rice using current techn ologies. An international effort has been established and is in the process of sequencing O. sativa spp, japonica var "Nipponbare" using a bacterial a rtificial chromosome/P1 artificial chromosome shotgun sequencing strategy. Annotation of the rice genome is performed using prediction-based and homol ogy-based searches to identify genes. Annotation tools such as optimized ge ne prediction programs are being developed for rice to improve the quality of annotation. Resources are also being developed to leverage the rice geno me sequence to partial genome projects such as expressed sequence tag proje cts, thereby maximising the output from the rice genome project. To provide a low level of annotation for rice genomic sequences, we have aligned all rice bacterial artificial chromosome/P1 artificial chromosome sequences wit h The Institute of Genomic Research Gene Indices that are a set of nonredun dant transcripts that are generated from nine public plant expressed sequen ce tag projects (rice, wheat, Sorghum, maize, barley, Arabidopsis, tomato, potato, and barrel medic). In addition, we have used data from The Institut e of Genomic Research Gene Indices and the Arabidopsis and Rice Genome Proj ects to identify putative orthologues and paralogues among these nine genom es.