A GEvo screenshot of a complete flanking gene analysis of a cluster of four potentially nonsyntenic Arabidopsis genes (enclosed in the oval) using both Cp (top) and Vv (middle) outgroups. In GEvo, when an HSP is clicked with the cursor, a line-of-synteny is drawn. For example, the orange HSPs and lines show clearly the one-to-one collinearity of the Cp and Vv outgroups, the most direct evidence for synteny. Note how the two flanking genes (indicated) in At each have hits to orthologous (syntenic) genes in both Cp (light brown) and Vv (dark brown). There are no runs of n’s between the flanking genes in either outgroup that could account for a missing gene. These four genes, including the PPR gene, were each transposed into this position in the At lineage.
