As I read through, I found a few interesting tidbits.
(a) the Universal Genome that encodes all major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs.
So, a couple of things that they found were:
While the presence of the opsins could be explained by their possible function in a simple light sensing, sea urchin has the entire set of orthologs of major genes involved in the eye development, e.g., Pax6, Six3, Prox1, Rx2 or Eya1 (NCBI database). Therefore, it appears that information on the eye development is encoded in the sea urchin genome, while no eye is actually developed, and thus the genetic information seems to be excessive.
Also, sea urchin has Rag1 and Rag2 genes that mediate the somatic rearrangement process common to both immunoglobulin and T cell‑antigen receptor gene families. In addition, other components that function in the reorganization and diversification of immunoglobulins and TCR have also been identified, including a polymerase homologous to the terminal deoxynucleotidyl transferase (TdT) and polymerase m.11 Yet, sea urchin does not have antibodies, and possibly lacks adaptive immunity in general. Genes that are seemingly useless in sea urchin but are very useful in higher taxons exemplify excessive genetic information in lower taxons.