Differential transcriptome analysis of the common shrimp Crangon crangon: Special focus on the nuclear receptors and RNAi-related genes

• 20 NRs and 31 RNAi-related genes were found in the common shrimp Crangon crangon.
• A novel RAR-like NR was discovered in female adult C. crangon.
• RNAi-core gene expression suggests that the necessary machinery for RNAi is present.
• Two distinct Sid-1 genes and Ago-2 genes were discovered.
• Rapidly evolving siRNA pathway core genes are probably linked to virus co-evolution.

The decapod Crangon crangon is one of the most valuable European fisheries commodities. Despite its economic importance, little sequence data is available for this shrimp species. In this paper, we report the transcriptome sequencing for five different stages of C. crangon (early embryo, late embryo, larva, female adults and male adults) and the annotation and stage-specific expression analysis of nuclear receptors (NRs) and RNA interference (RNAi)-related genes. The NRs are transcription factors that play an essential role in growth, development, cell differentiation, molting/metamorphosis and reproduction, while the RNAi-related genes are very important for internal gene expression regulation and in antiviral defense. We discovered a NR in the female C. crangon which is either a very rapidly evolved homolog of HR10, or a novel NR altogether. This new NR could act as a biological marker for sex determination as it is not expressed in male adults. Most RNAi-related genes were present in C. crangon, proving that the requirements for successful RNAi is present in this decapod shrimp. RNAi-based applications in Crangon such as its use in functional genomics or as antiviral therapeutics could become very important in the near future.