Embryonic development 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 urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and 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 embryonic and 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 embryonic and larval development. Temporal analysis suggests that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions.

可以说，胚胎发育是有机体一生中经历的最复杂的过程，而最好从系统角度来理解这种复杂性。海胆已经成为了解开发规范，形态发生和进化的极有价值的模式生物。海胆作为一种非卵形的氘代吻合器，在原虫和脊椎动物之间占有重要的进化生态位。变异三角藻（Lytechinus variegatus，Lv）是一种经过充分研究的大西洋物种，它为胚胎和幼体发育过程中的信号转导，模式和形态发生变化提供了重要的见识。太平洋种，Strytylocentrotus purpuratusus（Sp）是另一个经过深入研究的海胆，尤其是用于基因调控网络（GRN）和顺式调控分析的海胆。有一个注释良好的Sp基因组和转录组，但Lv尚未开发类似资源。在这里，我们提供了在胚胎和幼虫发育过程中11个时间点的Lv转录组的分析。时间分析表明，规范基础的基因调控网络在海胆物种中保存良好。我们表明，胚胎转录变异的主要转变将发育时间序列分为四个不同的，时间顺序的阶段。我们的工作表明，海胆的发育是通过相对稳定的基因表达状态的连续间隔发生的，这些状态被突然的转变所打断。