Transcriptional profiling of spiny lobster metamorphosis reveals three new additions to the nuclear receptor superfamily

Abstract

Background The Crustacea are an evolutionarily diverse taxon which underpins marine food webs and contributes significantly to the global economy. However, our knowledge of crustacean endocrinology and development is far behind that of terrestrial arthropods. Here we present a unique insight into the molecular pathways coordinating crustacean metamorphosis, by reconciling nuclear receptor (NR) gene activity from a 12-stage, 3-replicate transcriptome in the ornate spiny lobster (Panulirus ornatus) during larval development. Results We annotated 18 distinct nuclear receptor genes, including three novel NRs which are upregulated prior to metamorphosis and have hence been named the “molt-associated receptors” (MARs). We also demonstrate the ecdysone-responsive expression of several known molt-related NRs including ecdysone receptor, fushi-tarazu-F1 and E75. Phylogenetic analysis of the curated NR family confirmed gene annotations and suggested that the MARs are a recent addition to the crustacean superfamily, occurring across the Malacostraca from the Stomatopoda to the Decapoda. The ligand-binding domain of these receptors appears to be less conserved than that of typical group-1 NRs. Expression data from two other crustacean species was utilized to examine MAR expression. The Y-organ of the tropical land crab showed a decline in expression of all MARs from intermolt to post-molt. Tissue distributions showed gonad-enriched expression in the Eastern rock lobster and antennal gland-enriched expression in the tropical land crab, although expression was evident across most tissues. Conclusion By mining transcriptome data, we have curated an extensive list of NR genes expressed during the metamorphic molts of P. ornatus, including three novel crustacean NRs which appear to play a role in the molting process. Divergence of the E-region of these new receptors indicates that they may have adopted a function that is unconventional for NRs. Based on expression patterns, we can confirm that a number of NRs play a role in the ecdysone cassette which regulates molting in crustaceans. This study describes in detail the molecular events surrounding crustacean molting and metamorphosis by taking advantage of the distinctive life history unique to achelatan crustaceans. Electronic supplementary material The online version of this article (10.1186/s12864-019-5925-5) contains supplementary material, which is available to authorized users.

Double-Stranded RNA Binding Proteins in Serum Contribute to Systemic RNAi Across Phyla—Towards Finding the Missing Link in Achelata

“…Previously, lipoproteins and other lipid binding proteins have been implicated in nucleic acid binding and innate immunity, which is consistent with our results implicating them in dsRNA binding [33][34][35]52,53] (Table 1 and Figure 5). The dsRNA binding protein candidates identified in C. quadricarinatus, E. lanceolatus, and B. mori via mass spectrometry all share conserved functions in terms of lipid binding capacity, evidence of dsRNA binding, and links to innate immunity, but differ greatly in structure and size.…”

“…In E. lanceolatus, apolipoprotein A-1 was identified as the putative dsRNA binding protein. Apolipoprotein A-1 is known to possess antiviral activity and bind siRNA, while also being a prevalent serum protein [34,52]. These characteristics make it the most likely dsRNA binding protein identified in E. lanceolatus serum.…”

“…RNA was extracted from the 5th walking leg (which contained the androgenic gland) using the methodology described earlier by Hyde et al (2019) [59]. Briefly, the 5th walking leg tissue was mechanically homogenized in RNAzol ® RT reagent from the Molecular Research Center (Cincinnati, Ohio, United States) and 1% β-mercaptoethanol to prevent RNA degradation.…”

Multi-Tissue Transcriptome Analysis Identifies Key Sexual Development-Related Genes of the Ornate Spiny Lobster (Panulirus ornatus)

“…Sexual development factors identified in closely related species served as queries for tBLASTn search of the newly generated tissue transcriptome, as well as the previously generated metamorphic stage transcriptome [ 55 ]. Key factors known to be related to the sexual development pathway (defined in Section 1 ) were clearly identified in P. ornatus .…”

CrustyBase: an interactive online database for crustacean transcriptomes

“…During this time the animal goes through five molts, two of which involve a metamorphosis. This dataset was used to curate the nuclear receptor gene family and describe their activity throughout these developmental events [27]. We consider this a pilot dataset for CB and it will remain in the database with full public access (access levels are described in the Utility section).…”