IRGSP Build5 Pseudomolecules of the Rice Genome

We have updated the genome sequence of Oryza sativa ssp. japonica cultivar Nipponbare with the release of the Build 5 pseudomolecules representing the 12 rice chromosomes. The pseudomolecule for each chromosome was constructed by joining the nucleotide sequences of each PAC/BAC clone based on the order of the clones on the latest physical map. The overlapping sequences were removed and the physical gaps were replaced by successive Ns. The updated pseudomolecules were constructed based on the sequence data fixed on June 26, 2008. The nucleotide sequences of 7 new clones mapped on the euchromatin- telomere junctions were added in the new genome assembly. In addition, several clones in the centromere region of chromosome 5 were improved and one gap on chromosome 11 was closed.

The previous version of the IRGSP pseudomolecules (Build 4) was released in August 2005 and used as the common standard sequence for various analyses of the genome structure and function. These pseudomolecules also served as the template for manual curation of annotation in conjunction with the Rice Annotation Project Meetings (RAP2-RAP5).

The sequence data of the Build 5 pseudomolecules is currently available on the IRGSP website but will be submitted to public databases in due course. These pseudomolecules will be used to update the manually curated annotation of the rice genome in RAP-DB in the very near future. We hope that the scientific community will use the Build 5 pseudomolecules as the standard sequence of the rice genome and as a reference sequence for rice genomics.

The direction of sequence is from the short arm to the long arm of each chromosome.

chromosome no.
link to clone table
total lengthclone no.physical contig no.contig length (base)physical gap no.fasta file download
chromosome145,038,604bp392743,248,6046chr01.fasta.gz (13.4Mb)
chromosome236,792,247bp359535,932,2474chr02.fasta.gz (11.1Mb)
chromosome337,312,367bp329636,372,3675chr03.fasta.gz (11.3Mb)
chromosome436,060,865bp295635,520,8655chr04.fasta.gz (10.0Mb)
chromosome530,073,438bp286529,953,4384chr05.fasta.gz (9.2Mb)
chromosome632,124,789bp281331,244,7892chr06.fasta.gz (9.6Mb)
chromosome730,357,780bp290329,727,7802chr07.fasta.gz (9.1Mb)
chromosome828,530,027bp278228,440,0271chr08.fasta.gz (8.7Mb)
chromosome923,895,721bp223623,005,7215chr09.fasta.gz (7.0Mb)
chromosome1023,703,430bp203722,943,4306chr10.fasta.gz (7.1Mb)
chromosome1131,219,694bp258628,919,6945chr11.fasta.gz (8.9Mb)
chromosome1227,679,166bp269227,529,1661chr12.fasta.gz (8.4Mb)

last updated 2008.12.25