Abstract

The developmental program of each organism is encoded in the genome and is executed by large gene regulatory networks (GRN). In the last decade there has been a lot of study into GRNs for the development of various organisms, however, few systematic studies have been conducted to address the evolutionary mechanisms involved in shaping GRNs. We compare at the molecular level the development of the endoskeleton in two echinoderm classes (a sea urchin and a brittle star) that produce skeleton in both larval and adult stages and split at least 480 Mya. In our analysis we used transcriptome data, high-resolution spatio-temporal expression data and classical embryological observation. Despite the remarkable similarities of the tempo and mode of development between the brittle star Amphiura filiformis and the euechinoid (regular sea urchins) larvae, our high-resolution study of the dynamic of regulatory states highlights numerous differences in the architecture of the two GRNs. Interestingly, in A. filirmis the specification of the skeletogenic lineage does not rely on pmar1/hesC double negative gate, which is likely an euechinoid invention. Furthermore, the late regulatory states are significantly divergent due to the absence of expression of many regulatory genes in the A. filiformis skeletogenic lineage. We also identified several new downstream skeletogenic genes not present in sea urchin. Taken together our data show that gene duplications, protein function diversification and cis-regulatory elements evolution all contributed to shape the developmental GRN for larval skeletogenesis in different branches of echinoderms.