A possible explanation for this result could be that some of the scaffolds have been mapped and oriented with a BIN set comprised of a relatively low number of individuals.
In addition, the 158 scaffolds in the N90 index were mapped, ordered, and oriented (supplementary fig. S1, Supplementary Material online) using conserved linkage (Schaeffer et al. 2008), in situ hybridization, and additional information (González et al. 2005; Guillén and Ruiz 2012).
In addition, the 158 scaffolds in the N90 index were mapped to chromosomes, ordered, and oriented (supplementary fig. S1, Supplementary Material online; Delprat A, Guillén Y, Ruiz A, in preparation) using conserved linkage (Schaeffer et al. 2008) and additional information (González et al. 2005; Guillén and Ruiz 2012).
264 of these were mapped to intergenic regions oriented in antisense to neighboring genes but not overlapping the 5'- or 3'-UTRs and thus classified as type 1 trans-encoded sRNA candidates, whereas 721 were classified as type 2 sharing the same orientation as at least one of the two neighboring genes.
When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes.
The optical maps also allowed the assembled sequence scaffolds to be ordered and oriented (Table S3).
Physical map contigs placed within these regions similarly cannot be ordered and oriented in relation to other nearby contigs.
After mapping, contigs are ordered and oriented to produce even longer sequences called scaffolds, exploiting the mate-pair/paired-end information.
The scaffolds obtained from a de novo assembly were ordered and oriented solely by mapping BES based on the known physical map MTP order.
The fourth is the sequence-ready BAC/PAC physical map, and these BAC/PACs were anchored and oriented on the genetic map which forged a minimum tiling path of BAC/PAC clones for each of the 12 rice chromosomes – it comprises 3,466 BAC/PAC clones showing 46 gaps [ 8]. * Ch. = Chromosome; est.
