Transcriptomic analysis of light-induced genes in Nasonia vitripennis: possible implications for circadian light entrainment pathways

Circadian entrainment to the environmental day-night cycle is essential for the optimal use of environmental resources. In insects, opsin-based photoreception in the compound eye and ocelli, and CRYPTOCHROME1 (CRY1) in circadian clock neurons are thought to be involved in sensing photic information, but genetic regulation of circadian light entrainment in species without light-sensitive CRY1 remains unclear. To elucidate a possible CRY1-independent light transduction cascade, we analysed light-induced gene expression through RNA-sequencing in Nasonia vitripennis. Entrained wasps were subjected to a light pulse in the subjective night to reset the circadian clock and light-induced changes in gene expression were characterized at four different time points in wasp heads. We used co-expression, functional annotation, and transcription factor binding motif analyses to gain insight into the molecular pathways in response to acute light stimulus and form a hypothesis about the circadian light resetting pathway. Maximal gene induction was found after 2h of light stimulation (1432 genes), including the opsin opblue and the core clock genes cry2 and npas2. Pathway and cluster analyses revealed light activation of glutamatergic and GABA-ergic neurotransmission, including CREB and AP-1 transcription pathway signalling. This suggests that circadian photic entrainment in Nasonia may require pathways that are similar to mammals. We propose a model for hymenopteran circadian light resetting that involves opsin-based photoreception, glutamatergic neurotransmission, and gene induction of cry2 and npas2 to reset the circadian clock.

Methods
This dataset consists of all processed data needed to reproduce the analysis of RNAseq data from Nasonia vitripennis, published in Biology under the same title.

Data included here: the final transcriptome including final gene counts matrix, sample information file, functional annotation, GO annotation table, and other supplementary data described in the manuscript. 

The raw RNAseq reads can be found on the European Nucleotide Archive (ENA) under accession no. PRJEB57723.

All the scripts needed to process the data and reproduce the analysis can be found on GitHub at https://github.com/YFWang-YvH/Transcriptomic-analysis-of-light-induced-genes-in-Nasonia-vitripennis-implications-for-circadian.

Briefly: raw RNAseq reads were preprocessed and trimmed following the 'new Tuxedo' pipeline (see Pertea et al. 2016 Nature Protocols 11(9). This pipeline includes transcript assembly and quantification with StringTie, mapped to the newest Nasonia vitripennis reference genome “GCF_009193385.2_Nvit_psr_1.1_genomic.fna”. The final gene count matrix from StringTie is deposited here. The gene counts matrix and sample information file were used for further statistical analysis and the production of downstream datafiles and final figures shown in this manuscript. Please see the scripts on GitHub for pipeline and analysis details.