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

Abstract

In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up-regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.

Keywords: Mesocentrotus franciscanus; developmental transcriptome; early ontogeny; echinoderm; gene expression; larvae.

Figure 1

Gene Ontology categories for biological processes in the gastrula and pluteus transcriptomes of Mesocentrotus franciscanus. Categories are shown on the x‐axis; while the right y‐axis indicates the number of genes per category, the left y‐axis indicates the percentage of genes in the main category

Figure 2

Protein clusters among early developmental transcriptomes of echinoderms. (a) Comparison between gastrula and pluteus stages of Mesocentrotus franciscanus. Analysis of orthologous clusters among gastrulas (b) and pluteus (c) stages of the sea urchins M. franciscanus, Strongylocentrotus purpuratus and Lytechinus variegatus, the sea cucumber Parastichopus parvimensis (gastrula), and the brittle star Amphiura filiformis (pluteus)

Figure 3

Unigenes homology to KEGG genes obtained from the KAAS server. (a) Number of sequences assigned to each subcategory of the reference hierarchy KOs. (b) Percentage distribution of the five top KEGG orthology categories in the reference, gastrula, and pluteus transcriptomes of Mesocentrotus franciscanus

Figure 4

Gene expression profiles during early development of Mesocentrotus franciscanus. (a) Heat map generated from differentially expressed genes between gastrula and pluteus stages. The bar color reflects the gene expression levels. (b) Volcano plot displaying the log₂ fold change and the −log₁₀ of the p‐values from Kal's statistical test for the gastrula and pluteus stages. (c) Overview of log₂ expression ratios of all transcripts differentially expressed between gastrula and pluteus stages

Figure 5

Gene Ontology treemaps for annotated differentially expressed genes. (a) Up‐regulated GO terms in (a) gastrula and (b) pluteus stages of M. franciscanus. When GO terms are up‐regulated in gastrula, they are down‐regulated accordingly in the pluteus