The Essential Compendium to Eucidaris tribuloides: A morphological and transcriptomic characterization of embryogenesis

Abstract

Evolutionary development (evo-devo) is the study of how phenotypic changes occur through evolution as associated with developmental processes. This scientific discipline serves as a way to provide causal explanations into how changes in the genotype manifest as changes in a phenotype of an organism. An especially potent mechanism for explaining evolution of organismal development are gene regulatory networks (GRNs). GRNs are a summary of all the interactions between transcription factors, cis-regulatory elements, and signaling molecules that control how development proceeds. They are genetically encoded developmental instructions, and mutations of these sequences can have significant impacts in how the organization and function of animal body plans. Echinoderms have long served as morphological/genetic evo-devo study models, especially sea urchins for their unique biphasic life cycle and ease of experimental perturbation. Sea urchins, which belong to class Echinoidea, may be split into two subclasses: Euechinoidea, representing all modern sea urchins and sand dollars, and the basal sister group Cidaroidea, which contains all extant pencil sea urchins. Cidaroids act as a uniquely apt comparative model for evo-devo studies, as there is significant divergence between them and the euechinoids and clear morphological differences, yet together this clade in monophyletic. Despite these attractive characteristics, the vast majority of evo-devo studies have focused on a small handful of euechinoid sea urchins, which are all relatively closely related to one another, causing a phylogenetic gap in the current understanding of the evolution of development within Echinoidea. In this study, we sought to bridge this gap in knowledge by characterizing the developmental morphological and transcriptomic aspects of a cidaroid sea urchin Eucidaris tribuloides. In chapter 1, we developed the first standardized protocols for adult E. tribuloides adult husbandry and rearing conditions to bring E. tribuloides larvae to metamorphosis. We captured and described novel developmental stages, particularly those stages between the two-arm pluteus larvae and the metamorphosed juvenile, thus produced the first full developmental staging scheme for this cidaroid species. In an effort to understand how the differences during early development may impact the ontological trajectory of mesodermally derived tissues, we generated the first images of adult cidaroid coelomocytes. Taken together, the results of this chapter have established a morphological baseline of cidaroid development that will facilitate future comparative studies between these sea urchin species. In chapter 2, we produced both the first developmental transcriptome assembly (from cleavage stage to the two-arm stage) and the first gene annotations of any cidaroid sea urchin species. In total, we predicted 28,331 protein sequences with both homology and functional support. Several interesting patterns arose from these efforts. First, we were able to identify with high confidence a candidate E. tribuloides Pmar1 transcript, which provides evidence that Pmar1 existed within echinoids before divergence occurred. Second, of the 374 regulatory genes implemented in developmental control of S. purpuratus, we found 371 candidate genes in our cidaroid system, suggesting that most of these genes are deeply conserved within Echinoidea. Finally, it was observed that there is a heterochronic shift of the entire skeletogenic module within cidaroids, which supports the findings of previous studies and provides an excellent example of how changes in the regulation of tissue development can have profound phenotypic effects. The genetic resources we have generated in this chapter will serve as a powerful tool for future competitive studies investigating changes in echinoid development.