Cis-regulation and conserved non-coding elements in amphioxus

The origin of the vertebrates was a major event in the evolution of morphological diversity and the genetic mechanisms responsible for this diversity, once purely theoretical, can now be approached experimentally in the genome era. With a prototypical chordate genome, vertebrate-like development and simple morphology, amphioxus provides the appropriate model for investigating the origin of the vertebrates. Comparative genomics is revealing that both conservation and divergence of genes and cis-regulatory elements involved in developmental regulatory networks are required to shape different animal body plans. This article reviews the cis-regulatory studies performed in amphioxus, the discovery of conserved non-coding elements (CNEs) across the metazoans and the examination of amphioxus CNEs. Emerging ideas on the evolution of CNEs after large-scale genome duplication events and the state of cephalochordate genomics are also discussed.