What is a pseudomolecule, and how were they made?
The pseudomolecules were made by selecting an optimal tiling path of BAC and PAC clones that represent the 12 chromosomes. Overlaps between the BAC/PACs were trimmed and physical gaps are represented by a stretch of 1000 Ns. The centromeres were located due the gaps and presence of the CentO repeats. See here http://rice.plantbiology.msu.edu/annotation_pseudo_centromeres.shtml for the position of the centromeres. These overlapping clones were validated by comparison of the pseudomolecule sequence with the optical map for rice created by D. Schwartz of the University of Wisconsin. The pseudomolecules were error corrected using whole genome shotgun sequence of Nipponbare. Sequences from BACs and the Syngenta assembly of Nipponbare that could not be anchored are on separate pseudomolecules, the Unanchored and the Syngenta chromosomes. Assembly of this release of the pseudomolecules, termed Os-Nipponbare-Reference-IRGSP-1.0, were made in collaboration with the Agrogenomics Research Center
