Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms

Abstract

BackgroundThe mechanisms by which the conserved genetic “toolkit” for development generates phenotypic disparity across metazoans is poorly understood. Echinoderm larvae provide a great resource for understanding how developmental novelty arises. The sea urchin pluteus larva is dramatically different from basal echinoderm larval types, which include the auricularia-type larva of its sister taxon, the sea cucumbers, and the sea star bipinnaria larva. In particular, the pluteus has a mesodermally-derived larval skeleton that is not present in sea star larvae or any outgroup taxa. To understand the evolutionary origin of this structure, we examined the molecular development of mesoderm in the sea cucumber, Parastichopus parvimensis.ResultsBy comparing gene expression in sea urchins, sea cucumbers and sea stars, we partially reconstructed the mesodermal regulatory state of the echinoderm ancestor. Surprisingly, we also identified expression of the transcription factor alx1 in a cryptic skeletogenic mesenchyme lineage in P. parvimensis. Orthologs of alx1 are expressed exclusively within the sea urchin skeletogenic mesenchyme, but are not expressed in the mesenchyme of the sea star, which suggests that alx1+ mesenchyme is a synapomorphy of at least sea urchins and sea cucumbers. Perturbation of Alx1 demonstrates that this protein is necessary for the formation of the sea cucumber spicule. Overexpression of the sea star alx1 ortholog in sea urchins is sufficient to induce additional skeleton, indicating that the Alx1 protein has not evolved a new function during the evolution of the larval skeleton.ConclusionsThe proposed echinoderm ancestral mesoderm state is highly conserved between the morphologically similar, but evolutionarily distant, auricularia and bipinnaria larvae. However, the auricularia, but not bipinnaria, also develops a simple skelotogenic cell lineage. Our data indicate that the first step in acquiring these novel cell fates was to re-specify the ancestral mesoderm into molecularly distinct territories. These new territories likely consisted of only a few cells with few regulatory differences from the ancestral state, thereby leaving the remaining mesoderm to retain its original function. The new territories were then free to take on a new fate. Partitioning of existing gene networks was a necessary pre-requisite to establish novelty in this system.

Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins

“…Thus, in the early development of echinoids, the regulation of gcm changed markedly and at numerous nodes of the GRN; however, gcm still demarcates NSM polarity, which appears to be an echinoid novelty. This hypothesis is supported by the observation that no significant polarity occurs during embryonic mesodermal specification of asteroids, ophiuroids, and holothuroids (95)(96)(97). Thus, polarization of gcm and ese is a derived feature of echinoids that likely first appeared at least 268 mya, and the mechanism of NSM segregation via Nodal/SMAD signaling is likely conserved since that time (Fig.…”

Gene expression profiling during the embryo‐to‐larva transition in the giant red sea urchin Mesocentrotus franciscanus

“…However, differences in skeleton formation and embryonic territories specification in this group are the result of evolutionary changes, which include gene duplications, protein function diversification, and genes co‐opted to different functions (Dylus et al., 2016; Hinman & Davidson, 2007; Hinman, Nguyen, Cameron, et al., 2003; McCauley et al., 2010, 2012). Here, comparisons of early developmental transcriptomes of echinoderms revealed several proteins/genes that are highly conserved among sea urchins, sea cucumbers, and brittle stars (Figure 2b,c).…”

“…Despite the differences in larval development in this group (e.g., pluteus‐, bipinnaria‐, and auricularia‐like larvae), comparisons of their GRN architectures have detected highly conserved orthologous regulatory genes among the extant echinoderm classes (Hinman & Davidson, 2003a,b; Hinman, Nguyen, Cameron, & Davidson, 2003; Hinman, Nguyen, & Davidson, 2003). While the network logic employed is the same in these organisms, the transcription factors underlying certain functions have been the subject of evolutionary change, resulting in gene duplications, protein function diversification, and regulatory genes co‐opted to different functions (Dylus et al., 2016; Hinman & Davidson, 2007; Hinman, Nguyen, Cameron, et al., 2003; McCauley, Weideman, & Hinman, 2010; McCauley, Wright, Exner, Kitazawa, & Hinman, 2012). …”

Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

“…The holothurian P. parvimensis was developed as an experimental developmental system only recently, once improved methods for spawning animals were established (38,39). Those earlier studies revealed that P. parvimensis has an alx1-expressing PMC-like cell lineage that produces a small larval spicule.…”

“…Those earlier studies revealed that P. parvimensis has an alx1-expressing PMC-like cell lineage that produces a small larval spicule. This lineage arises in the vegetal pole, and, before ingression, alx1 is coexpressed with holothurian tbr, ets1, and erythroblast transformation specific ets-related gene (erg) orthologs (38). The expression of hesc, and indeed any earlier mechanisms that might lead to the specification of this lineage at the vegetal pole of P. parvimensis, were not determined, however.…”