Developmental Single-cell transcriptomics in the Lytechinus variegatus Sea Urchin Embryo

Abstract

<jats:title>Abstract</jats:title><jats:p>Here we employed scRNA-seq coupled with computational approaches to examine molecular changes in cells during specification and differentiation. We examined the first 24 hours of development of the sea urchin <jats:italic>Lytechinus variegatus</jats:italic> (<jats:italic>Lv</jats:italic>) with 18 time points during which the embryo develops to the larval stage. Using Waddington-OT, the time points were computationally “stitched” together to calculate developmental trajectories. Skeletogenic cells displayed the expected immediate early divergence while other lineages diverged asynchronously, with many cells retaining an intermediate specification status until late in gastrulation. The <jats:italic>Lv</jats:italic>-scRNA-seq dataset was compared to the developmental Gene Regulatory Network (dGRN) model of specification in <jats:italic>Strongylocentrotus purpuratus</jats:italic> (<jats:italic>Sp</jats:italic>). 79 of 80 genes (98%) in that dGRN are present in the <jats:italic>Lv</jats:italic>-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate. Surprisingly, however, many heterochronies in timing of first expression of dGRN genes have evolved between the two species. Replotting the two dGRNs with precise attention to time of expression revealed a number of feedback inputs that likely buffer the dGRNs, allowing them to maintain function in the face of accumulating heterochronies.</jats:p><jats:sec><jats:title>Summary statement</jats:title><jats:p>The early development of the sea urchin embryo was followed using scRNA-seq plus computational methods to trace lineage diversifications. These were matched to gene regulatory network changes over time.</jats:p></jats:sec>