The Developmental Transcriptome for Lytechinus variegatus Exhibits Temporally Punctuated Gene Expression Changes

Embryonicdevelopment is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchinhas become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non- chordate deuterostome, the sea urchinoccupies an important evolutionary niche between protostomesand vertebrates. Lytechinus variegatus(Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonicand larval development. The Pacific species, Strongylocentrotus purpuratus(Sp), is another well-studied sea urchin, particularly for gene regulatory networks(GRNs) and cis-regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonicand larval development. The data indicate that the gene regulatory networksthat underlie specification are well-conserved among sea urchinspecies. We show that the major transitions in variation of embryonictranscription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchindevelopment occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions.