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The Academia Sinica Plant Genome Center has completed sequencing and finishing of rice chromosome 5 genome, have been cover 99.1% of the mapped BAC/PAC clones. The minimal tiling path (MTP) for chromosome 5 consisted of 279 BAC clones. Assembly of the sequences of these clones constructs a pseudomolecule of 29 Mb in length; only 4 physical gaps have to mapped and sequenced. The progress of sequencing and finishing in each rice chromosome can be found at the IRGSP web site: http://rgp.dna.affrc.o.jp/IRGSP/indes.html
Genome sequencing project of rice chromosomes
Rice has been chosen as the first crop genome sequencing by an international rice genome sequencing consortium, IRGSP (International Rice Genome Sequencing Project) for the following reasons:
- rice is an important crop in the world;
- the genome size of rice is 430 Mb, the smallest one among crops;
- linkage maps and physical maps of rice have been established and more than 70,000 rice EST sequences have been registered;
- the transgenic rice technology has been established;
- rice shares a co-linear gene organization with other cereal grasses, thus rice is a key to knowledge of the genomic organization of the other grasses.
There are 12 chromosomes in rice. Ten countries agree to joint the IRGSP. The chromosomal assignments are as follows : Chrom. 1, Japan; Chrom. 2, Japan and UK; Chrom. 3, USA; Chrom. 4, P.R. China; Chrom. 5, Taiwan; Chrom. 6, Japan; Chrom. 7, Japan; Chrom. 8, Japan; Chrom. 9, Japan, Thailand, Korea and Brasil; Chrom. 10, USA; Chrom. 11, USA and India; Chrom. 12, France.
General outline
A sequencing project to sequence rice chromosome 5, about 32 Mega-base, have been supported by the Academia Sinica, National Science Council, Council of Agriculture and the Institute of Botany, Academia Sinica since March, 1999. Decoding of the rice genome by IRGSP members has come to the final stages, and completed as a hight-quality draft (phase 2) in December, 2002. This major project has involved collaboration among ten countries and with input from scientists in a wide spectrum of disciplines. In ASPGC we are collaborated with National Yang-Ming University and VitaGenomics Co. for high-through put sequencing in 2002 to finish chromosome 5 genome and sequenced more than 300 BAC clones on a fine physical map for a total of 32 Megabases.
Progress and Accomplishments
 A fine physical map with a total of 279 BAC/PAC clones on the milimal tiling path (MTP) for chromosome 5 of rice have been constracted. Asembly of sequences from each BAC/PAC clone on MTP has come to a high quality phase 2 sequences draft in 2002. Finishing of the phase 2, the orderedcontigs, to a completed sequences (phase 3) started this year and will completed finishing work and annotation of genes by the end of 2004. We are now finishing, BAC by BAC, by re-sequence of low quality region and fill the gaps by re-sequence of the bridge-clones or by primer walking. The progress of finishing among 12 chromosomes are monitored by IRGSP on a weekly-progress report and monthlyprogress report basis and notified to all collaborative genome centers. Progress of chromosome 5 finishing in ASPGC could be found on the web site: http://genome.sinica.edu.tw
The Academia Sinica Plant Genome Center is supported by Academia Sinica, Institute of Botany, National Science Council, and Council of Agriculture. The main project is genome sequencing project of rice chromosome 5. Several themes are also included in the research fields currently, including the EST projects of certain local plants, SAGE analysis of developing rice seeds as well as FST analysis of a T-DNA insertional ice mutant population, etc. |
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