Flanking Gene Method

GEvo analysis showing the flanking gene method. The top panel represents a transposition event in one species as compared to uninterrupted genes in the orthologous region of another species in the panel below

The flanking gene method is a procedure in which possible transposed genes are identified by comparing two neighboring syntenic gene pairs. An example visualization of this method is shown to the right. In this visualization, a pair of genes (numbered 1 and 2) in Species A is being compared to an orthologous pair of genes (similarly numbered 1 and 2) in Species B.

In the procedure, sequential, adjoining genes (genes 1 and 2) are compared between two species (A and B). If said genes are from orthologous regions, one would assume the genes remain sequential. However, in a transposition event another gene (eg, gene X in red) inserts itself between two otherwise sequential genes. In this case, gene X is a possible transposed gene, identified by its presence in Species B between genes 1 and 2 which would be otherwise adjoining each other. This method of identification is previously described in Freeling et al 2008.

Further analysis uses an additional species as an outgroup to determine whether or not gene X is, in fact, an insertion between genes 1 an 2 rather than merely a gene in sequence that's been deleted.