Amphioxus functional genomics and the origins of vertebrate gene regulation

Vertebrates have greatly elaborated the basic chordate bodyplan and evolved highly distinctive genomes, sculpted by two whole genome duplications (WGD). To investigate the evolution of genome regulation in chordates, we characterized promoters, DNA methylation, chromatin accessibility, histone modifications and transcriptomes in multiple tissues and throughout development of amphioxus. This revealed an intermediate stage in the evolution of differentially methylated regulatory elements, and high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates, maximally at an earlier mid-embryonic phylotypic period. We also unraveled the principal route of regulatory evolution following vertebrate WGDs: over 80% of broadly expressed gene families with multiple WGD-paralogs in vertebrates have members that restricted their ancestral expression, undergoing specialization rather than subfunctionalization. Counter-intuitively, vertebrate genes that underwent expression restriction increased the complexity of their regulatory landscapes. Altogether, these data pave the way for a better understanding of the regulatory principles underlying key vertebrate innovations