Evolution of the embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.
Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages.\n\nHere, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns.\n\nWe find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. In most cases, chromatin accessibility is not temporally regulated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of \"shadow\" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of the trans-regulatory logic between these distantly-related ascidians and. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.\n\nHIGHLIGHTSO_LIOpen chromatin regions are highly enriched for cis-regulatory elements in ascidian early embryos.\nC_LIO_LIAscidian Clusters of Open Regulatory Elements (COREs) are found next to regulatory genes.\nC_LIO_LIRegulatory gene expression, the trans-regulatory code, is conserved between distantly-related Ciona and Phallusia ascidians.\nC_LIO_LIAscidians show pervasive use of \"shadow\" enhancers\nC_LIO_LIThe position of homologous enhancers can be conserved, despite extensive genome divergence.\nC_LI