Figure 2.

Rearrangement scenario showing one possible explanation of differences observed in the Welwitschia SSC region. Gene order and orientation are represented in the diagram, but genes and IGS are not shown to scale. Map 1 shows the SSC and flanking ends of the IR as the region appears in Cycas or Ginkgo, maps 2–6 are hypothetical, and map 7 illustrates the region as it appears in the Welwitschia genome. Event a is an inversion that reverses the orientation of trnN. One endpoint of this inversion may have disrupted ndhF, leading to its loss. Event b is an inversion that reverses chlN. One endpoint may have disrupted chlL. Event c is the copy correction of the second IR copy to reflect the gene order change (event a) in the other copy. Events d, e, and f are inversions modifying the order and orientation of blocks of genes within the SSC. Again, in step e, inversion breakpoints may have disrupted genes. Events g, h, and i are additional gene losses (chlN is still detectable as a pseudogene) not directly related to inversion breakpoints. Event j is an extension of the inverted repeat into the SSC to copy rpl32 into the IR. The positions of the inversion endpoints are defined by the gene adjacencies in Welwitschia as compared to the ancestral condition, however exactly how those endpoints are combined into inversion events is speculative. Thus the endpoints indicated for events b-f may have been combined in different ways and the events may have occurred in an alternative order than that represented in this model.