Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats
A model of a transposed gene surrounded by flanking repeats, based on the graphics of our genome visualization platform GEvo (http://synteny.cnr.berkeley.edu/CoGe/GEvo.pl). The middle panel represents the transposed gene (yellow), the top panel represents the sequence in A. lyrata that is the orthologous region to the transposed gene locus, and the bottom panel represents the parental site in A. thaliana from which the mobile gene transposed. The long red rectangles above the genes in the top and middle panels represent orthologous sequence between A. thaliana and A. lyrata; the long blue rectangles in the middle and bottom panels represent sequence similarity between the transposed A. thaliana gene and the parent gene of origin. Purple arrows beneath the sequence represent direct repeats in A. thaliana and the sequence homology between the direct repeats in A. lyrata. Circled are the repeated sequences that are similar among the A. thaliana parental site, the transposed gene, and the target site in A. lyrata (note that the sequence only appears once in the A. lyrata target site). This model suggests that the repeat sequence flanking the transposed gene (circled rectangles, center panel) is a chimera between the donor site repeat sequence and the A. lyrata target site (also see Figure 3B). Notice that the parent site is a tandem duplication.