IRGSP Releases Build 4.0 Pseudomolecules of the Rice Genome
The International Rice Genome Sequencing Project (IRGSP) has updated the genome sequence of Oryza sativa ssp. japonica cultivar Nipponbare with the release of the Build 4.0 pseudomolecules. The nucleotide sequence representing the entire chromosome was constructed by joining the sequence 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 previous version of the pseudomolecules (Build 3.0) was released in February 2005. These sequences were used as the common standard for various analysis of the genome, which were published in the Nature (436:793-800,2005). The Build 3.0 pseudomolecules also served as the template for manual curation of annotation in conjunction with the First Rice Annotation Project Meeting (RAP1) which was held in Tsukuba, December 13-18, 2004. The RAP1 database will be released soon.
The Build 4.0 pseudomolecules were constructed based on the data freeze on Jan 25, 2005. The sequence data is currently available on the IRGSP website but will be submitted to the public databases in due course.
The IRGSP recognizes that the Build 4.0 pseudomolecules is the official standard sequence of the genome of and hopes that the scientific community will use it as a reference sequence for rice genomics. These pseudomolecules will be used to update the manual curation of annotation as part of the Second Rice Annotation Project Meeting (RAP2), which will be held in Manila this November and in Tsukuba next February.
The direction of sequence data for each chromosome is (from the short arm to the long arm).
chromosome1 (45,064,769bp), chr01.gz (13.3Mb)
chromosome2 (36,823,111bp), chr02.gz (11.0Mb)
chromosome3 (37,257,345bp), chr03.gz (11.1Mb)
chromosome4 (35,863,200bp), chr04.gz (10.8Mb)
chromosome5 (30,039,014bp), chr05.gz (9.1Mb)
chromosome6 (32,124,789bp), chr06.gz (9.5Mb)
chromosome7 (30,357,780bp), chr07.gz (9.1Mb)
chromosome8 (28,530,027bp), chr08.gz (8.7Mb)
chromosome9 (23,843,360bp), chr09.gz (7.0Mb)
chromosome10 (23,661,561bp), chr10.gz (7.0Mb)
chromosome11 (30,828,668bp), chr11.gz (8.7Mb)
chromosome12 (27,757,321bp), chr12.gz (8.4Mb)