How can comparison of syntenic genomic regions help in gene annotation?

Figure 1 shows an example of comparing a region of papaya to its syntenic regions in Arabidopsis where there is probably an error in the Arabidopsis gene annotation. By comparison to papaya, it is clear that there are two loci as evidenced by an inversion.

Figure 1. Comparison of papaya to syntenic regions in Arabidopsis using blastz. Regions of sequence similarity between At1 and At2 are pink, At1 and Papaya are red, and At2 and Papaya are blue. Notice that At2 has a region marked as one gene while At1 has the region marked as two (red boxes and lines, underlying gene models). Papaya has sequence similarity to both these regions, but one region is inverted as shown by the HSPs drawn on the lower strand. This inversion to papaya combined with transcript evidence (blue region in gene models in At1) indicate that At2's gene annotation is likely incorrect.