Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris

Abstract

The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.

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

“…For sea urchins, these GRNs are represented by over 200 experimentally verified regulatory interactions acting during early development, from the unfertilized egg through the formation of a planktonic feeding larva (Israel et al., 2016). In our study, we identified ~2,600 functional, structural, and regulatory genes in M. franciscanus involved in developmental process (GO:0032502).…”

“…These processes are modulated by subcircuits of genes encoding transcription factors and their linkages (Israel et al., 2016). In our study, we were able to identify genes related to transcription regulatory activity (91:420; GO:0030528), transcription factor complex (143:533; GO:0005667), and transcription factor binding (249:241; GO:0008134) in the gastrula and pluteus transcriptomes (Table S8).…”

“…The disparity in the number of genes for some of these GO terms between both transcriptomes (Pearson Chi‐square test, p  < .05; Table S2) could reflect differences in the time of specification and differentiation of cell types (e.g., endomesoderm vs. neural cell types), and also sequential activation of genes in a regulatory hierarchy (Wei et al., 2006). In fact, in our analysis, some genes related to the determination of left/right symmetry (GO:0007368) were only present in the pluteus transcriptome (Table S7), supporting the idea of time‐dependent processes associated with GRNs (Israel et al., 2016). Overall, the most abundant transcription factors in early stages of M. franciscanus were associated with the FOX (Forkhead box), E2F, and HES (Hairy and enhancer of split) families, followed by the CCR4‐NOT complex, the TFIIA (transcription initiation factor iia), and the CREB (cAMP response element‐binding protein) proteins (Table S8 and Fig.…”

“…S4). In conjunction, the expression of these genes and other developmental regulators determine the progressive changes in form that characterize the embryo‐to‐larva transition in sea urchins (Dylus et al., 2016; Israel et al., 2016; McCauley et al., 2010; Rafiq et al., 2012, 2014; Wei et al., 2006). …”

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

“…I conducted comparative clustering analyses to identify statistical differences in timecourse data (79,80). By clustering Sp regulatory orthologs into six distinct clusters and forcing assignment of each Et ortholog into all clusters, cluster membership scores and clustering similarities for each ortholog were acquired (SI Appendix, Tables S3-S5).…”