A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus

Abstract

RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to trigger effective silencing, with a notable exception in the spiny lobsters where repeated attempts at dsRNA induced RNAi have demonstrated extremely ineffective gene knockdown. A comparison of the core RNAi machinery in transcriptomic data from spiny lobsters (Panulirus ornatus) and the closely related slipper lobsters (Thenus australiensis, where silencing is highly effective) revealed that both lobsters possess all proteins involved in the small interfering and microRNA pathways, and that there was little difference at both the sequence and domain architecture level. Comparing the expression of these genes however demonstrated that T. australiensis had significantly higher expression in the transcripts encoding proteins which directly interact with dsRNA when compared to P. ornatus, validated via qPCR. These results suggest that low expression of the core RNAi genes may be hindering the silencing response in P. ornatus, and suggest that it may be critical to enhance the expression of these genes to induce efficient silencing in spiny lobsters.

Tropical rock lobster (Panulirus ornatus) uses chemoreception via the antennular lateral flagellum to identify conspecific ecdysis

“…Functional assessment of IRs in chemosensory behaviour has been achieved through RNA interference (RNAi) knock-out of IR25a and IR93a in several Daphnia species 60 . In the case of P. ornatus , reverse genetic studies with RNAi have proven to be ineffective, due in part to animal-wide low expression of the enzymes and receptors required for functional and systemic gene silencing 61 . Despite multiple attempts to generate clear phenotypes with RNAi in P. ornatus and other Palinurid lobsters, no significant silencing has ever been observed which limits the functional annotation of ORNs in spiny lobsters.…”

Knock down to level up: Reframing RNAi for invertebrate ecophysiology

“…Some of these challenges are difficult to overcome in species that are recalcitrant to RNAi. For example, spiny lobsters (Panulirus ornatus) have low RNAi efficacy and expression of Dicer and Argonaute compared to their close (and amenable-to-RNAi) relative, slipper lobsters (Thenus australiensis; Banks et al, 2022Banks et al, , 2020. However, other challenges can be overcome by modifying your RNAi protocol.…”