Methods of genome assembling
All of the sequences of BAC/PAC/Fosmid clones as well as PCR products of the Nipponbare genome were determined by ex officio members of the IRGSP. The clones were first ordered on the basis of a physical map. The overlaps between the clones were identified by a custom-made Perl script that detected identical nucleotide matches. Sequencher (version 3.1.1, Gene Codes) was used to find non-perfect matches between the clone sequences. For the sequences of the non-perfect match regions, those of higher quality in terms of the sequence phase were selected. If two overlapping regions had the same quality, the north clone was employed. The lengths of all gaps were estimated by the fiber-FISH method1. A list of the clones and gaps can be downloaded form the download page.
To check the orders and orientations of the clones, genetic markers2 and EST markers3 were mapped to the genome assembly and errors were corrected.
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436: 793-800 (2005)
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[PubMed] - Wu et al. "A Comprehensive Rice Transcript Map Containing 6591
Expressed Sequence Tag Sites" Plant Cell 14: 525-535 (2002)
[PubMed]