NAR Molecular Biology Database Collection entry number 79

http://rgp.dna.affrc.go.jp/giot/INE.html

Matsumoto, T.¹, Mukai, Y.¹, Namiki, N.¹, Sakai, Y.², Makino, K.², Sakata, K.², Antonio, B.¹, Sasaki, T.¹

¹Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences / Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305, Japan
²Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan

Contact tsasaki@nias.affrc.go.jp

The rice genome database INE (INtegrated rice genome Explorer) is a rice integrated database with a browser for all the genomic information that have been accumulated from the large-scale rice genome analysis including cDNA analysis, genetic mapping, physical mapping and the ongoing rice genome sequencing project. A total of 481 Mbp of rice genomic sequence data (as of Sept. 2004) from 3,454 PAC/BAC and newly constructed fosmid clones has been incorporated in the database as a result of an extensive effort of the International Rice Genome Sequencing Project (IRGSP) to accelerate the completion of gettingthe genome sequence. Since the IRGSP comes very near to the goal ofcompletion, INE, which serves as the central database of IRGSP, currently contains almost 370 Mbp of non-overlapping sequence corresponding to about 95% of the entire rice genome. The sequence data areintegrated with the genetic map, a YAC (yeast artificial chromosome)-based physical map, transcript map, PAC (P1-derived artificial chromosome) / BAC (bacterial artificial chromosome) contigs for each sequenced clone. This map-based information of the sequence data would be very useful in elucidating the structure and function of specific regions of the genome particularly those containing agronomically important genes.

In 2002, RGP has finished sequencing of chromosome 1, the longest chromosomein the genome (Sasaki et al. 2002), followed by the analysis of chromosome 4 by the NCGR of Chinese Academy of Sciences (Feng et al. 2002), and chromosome 10 by US rice genome sequencing consortium (2003). At present the remaining nine chromosomes are almost completedand the finished sequences from PAC/BAC/fosmid clones are incorporated in INE. INE is also linked to the sequence annotation information. RGP is assigned for sequencing and annotation of chromosomes 1,2,6,7,8, and 9. In 2003, sequences from the rice full-length cDNAs were presented (The rice full-length cDNA consortium, 2003). The mapped cDNAs are the powerful resources for model construction of the evidenced genes. RGP has revised the system of manual curation ofthe predicted genes with the emphasis on the mapped cDNAs. For almost all the PAC/BAC clones aligned in chromosomes 2, 7, 8, and most part of 9 and half of chromosome 6, results of the manual curationof the genome sequences for the precise prediction of gene domain are presented. The RGP is also proceeding the re- annotation in which the gene models are revised with the updated information. For theclones of other six chromosomes, that are chromosomes 3,4,5,10,11, and 12, results of rice automated annotation system (RiceGAAS, Sakata et al, 2002) are presented with the finished genome sequence. Thus INE will continue to provide a system for consolidating all thegenome sequence data accumulated by the IRGSP as well as all relevant information to be elucidated from analysis of the genome sequence. INE can be accessed at http://rgp.dna.affrc.go.jp/giot/INE.html.

1. Integration of the sequence data corresponding to 95% of rice genomefrom the international sequencing effort.
2. Completion of the sequencing for almost all the chromosomes and access to the sequence data.
3. Annotation data for all the PAC/BAC clones are displayed. Revision of thecuration system based on rice full-length cDNA sequences was performed and results of the curation are shown for all the clonesalignedin chromosomes 2,6,7,8, and 9.
4. Re-annotation of the chromosome 1 sequences are successively incorporated.

INE was developed and maintained by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project GS-1302).

1. Sasaki et al. 2002. The genome sequence and structure of rice chromosome 1. Nature 420:312-316.
2. Feng et al. 2002. Sequence and analysis of rice chromosome 4. Nature 420:316-320.
3.The Rice chromosome 10 sequencing consortium. 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566-1569.
4. The rice full-length cDNA consortium 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376-379.
5. Sakata et al. 2002. RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Research 30:98-102.

Go to the abstract in the NAR 2000 Database Issue.

Oxford University Press is not responsible for the content of external internet sites