Plant Genome IV Conference Plant Genome IV Conference
In rice genome, approximately 20,000 - 40,000 protein genes are estimated to be expressed. Cataloging of all these expressed genes in rice is one of the final goal of the large scale cDNA analysis in RGP. Toward this goal, we have partially sequenced more than 27,000 cDNA clones isolated from various tissues of rice (Nipponbare, a japonica variety): root, green shoot, etiolated shoot, panicles and four types of cultured cells. Already sequence data of 10,990 clones has been released through the DNA Data Bank of Japan (DDBJ), GenBank and EMBL. The sequenced clones have also been used as ESTs on rice RFLP linkage map and for the construction of a physical map using YAC contigs. The similarity search to PIR database using FASTA algorithm showed that only 25% of the clones had significant similarities to known proteins. Thus, most of obtained clones could be considered as encoding functionally unknown proteins. To classify these "unknown clones" (cDNA clone with a sequence of unknown function), their nucleotide sequence data were examined by using the BLAST algorithm. Total of 22,287 clones were classified into 9,598 groups. Several "unknown clones" were classified into the same groups with clones putatively identified as known proteins. On the other hand, there were groups that contained only "unknown clones", and some of these groups were found only in specific libraries. This type of investigation is expected to provide useful information on gene expression and gene regulation mechanisms in rice.