Fig. 4

Synthesizing syntenic analysis information across target genomes: UNA classes. On the left is the Brassicaceae family tree. On the right, is the syntenic context for an imaginary query gene versus each target species. The query gene matches a gene in the most closely related target species, so is classified as AAic (A). In Cr, there is evidence of an indel, but no positive evidence for presence/absence of the gene in the species, so it is labeled as Unknown (U). The most distant branch from the focal species contains two species, one of which contains a positive NTic match and for other data is possibly missing. Since it is possible that an AAic match exists in Es, the branch is classified as Unknown overall. These three labels (A, N, and U) are a qualitative indication of the support for a gene being present along each cousin branch. The query gene is certainly not an orphan gene, but more precise statements are not justifiable. Including more target species could support a stronger inference for the query gene origin. This figure illustrates comparison at the species level. As more sub-species genomes are sequenced, we recommend inclusion of lineages within the focal species for a more powerful analysis, and for improved ability to distinguish rapidly evolving orphans from de novo orphans