Sequence Assembly Validation: Examining Gene Order in Physical Maps Versus Sequence Assembly

The gene order of the chloroplast genome of Podocarpus macrophylla has been determined twice -- once by shotgun sequencing, and, with a different sample, once by physical mapping. Although the gene order should be the same regardless of method, these two gene maps are inconsistent � a large region of genes is inverted in one map relative to the other. It is possible that the sequence-based map is incorrect, since mapping using sequence data is indirect, and because various attributes of sequence data can sometimes lead to misassembly causing inversions in maps. However, it is also possible that there was a true difference between the genomes of the two samples. Therefore, I am preparing a physical map using the Podocarpus macrophylla DNA sample, in order to compare directly a physical map and the sequence-based map. I have designed a physical mapping strategy that uses restriction enzymes that will generate distinct fragment patterns when the enzyme-digested Podocarpus DNA is run on a gel using electrophoresis. Depending on which set of fragments I recover I will be able to determine which gene order is actually correct