Fig. 5.

Proposed scenario of SFZE evolution and the origin of the notochord.

The SFZE syntax (red rectangles) associated with brachyury orthologs could have already been present before the emergence of animals. The regulatory network that activates brachyury in the axial mesoderm by concurrent Nodal and FGF signals through the SFZE syntax may have been established in the chordate lineage, at least before the divergence of tunicates and vertebrates. The Ets and Fox family factors (activated by yet to be determined signaling pathways, indicated by question marks) likely regulate brachyury expression through SFZE in at least ambulacrarians. Some components of the regulatory inputs could have been modified due to the loss of nodal and/or foxh genes in Drosophila and ambulacrarians (cross symbols). After two rounds of whole-genome duplications (2R), the SFZE syntax remained associated with both brachyury paralogs. Other notochord enhancers (T3/C/I) were subsequently evolved to control one of the paralogs (i.e., tbxb). In tetrapods, only tbxb was retained, and the notochord activity of the mammalian SFZE may have been substituted by T3/C/I enhancers. Created in BioRender. Fan, T. (2025) https://BioRender.com/14o3zg1.