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..., 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..., File extensions of the deposited data files include .gtf, .stats, .txt, and .csv. These are all text-based file formats that can be opened with any text processor. , Provenance for this README --- * File name: README.MD * Authors: Yifan Wang * Other contributors: Bregje Wertheim, Leo W. Beukeboom, Roelof A. Hut * Date created: 2022-12-31 Dataset Version and Release History --- * Current Version: * Number: 1.0.0 * Date: 2023-02-14 * Persistent identifier: * Summary of changes: n/a Dataset Attribution and Usage --- * Dataset Title: Data for the article \"Transcriptomic analysis of light-induced genes in Nasonia vitripennis: possible implications for circadian light entrainment pathways\" * Persistent identifier: DOI * Dataset contributors: Yifan Wang, Leo W. Beukeboom, Bregje Wertheim, Roelof A. Hut * Dataset citation: \> Wang\, Y\, Contact Information --- * Name: Yifan Wang * Affiliations: Evolutionary genetics group, Groningen Institute for Evolutionary Life Sciences, University of Groningen * ORCID ID: https://orcid.org/0000-0002-6541-7435 * Email: [e-mail] * Alternate Email: [e-mail] * Address: e-mail ...生物钟对环境昼夜节律的同步，对于高效利用环境资源至关重要。在昆虫中，复眼与单眼中基于视蛋白的光感受，以及生物钟神经元中的隐花色素1（CRYPTOCHROME1, CRY1）被认为参与光信号感知，但对于缺乏光敏CRY1的物种，其生物钟光同步的遗传调控机制仍不明确。 为阐明潜在的不依赖CRY1的光转导通路，我们通过RNA测序（RNA-sequencing）分析了丽蝇蛹集金小蜂（Nasonia vitripennis）中光诱导的基因表达。我们将已完成生物钟同步的寄生蜂置于主观暗夜中施加光脉冲以重置其生物钟，并在寄生蜂头部的四个不同时间点对光诱导的基因表达变化进行了表征。我们通过共表达分析、功能注释以及转录因子结合基序分析，解析了响应急性光刺激的分子通路，并提出了关于生物钟光同步……的假说。 本数据集包含用于复现丽蝇蛹集金小蜂RNA测序数据分析所需的全部处理后数据，相关研究成果以同名发表于《Biology》期刊。 本数据集包含以下内容：最终转录组（含基因计数矩阵）、样本信息文件、功能注释文件、基因本体（Gene Ontology, GO）注释表，以及论文中提及的其他补充数据。 原始RNA测序读数可在欧洲核苷酸档案馆（European Nucleotide Archive, ENA）获取，登录号为PRJEB57723。 所有用于数据处理与分析复现的脚本，可于GitHub平台获取，链接为：https://github.com/YFWang-YvH/Transcriptomic-analysis-of-light-induced-genes-in-Nasonia-vitripennis-implications-for-circadian。 简要说明：原始RNA测序读数按照“新Tuxedo”流程进行预处理与剪切（详见Pertea等人2016年发表于《Nature Protocols》第11卷第9期的研究）。该流程涵盖使用StringTie进行转录组组装与定量，并将结果比对至最新版丽蝇蛹集金小蜂参考基因组“GCF_009193385.2_Nvit_psr……”。 本数据集所存数据文件的扩展名包括.gtf、.stats、.txt与.csv，均为基于文本的文件格式，可通过任意文本编辑器打开。 ### 本README文件来源 * 文件名：README.MD * 作者：王一帆 * 其他贡献者：Bregje Wertheim、Leo W. Beukeboom、Roelof A. Hut * 创建日期：2022-12-31 ### 数据集版本与发布历史 * 当前版本： * 版本号：1.0.0 * 发布日期：2023-02-14 * 持久化标识符： * 变更概要：无 ### 数据集归属与使用说明 * 数据集标题：《丽蝇蛹集金小蜂光诱导基因的转录组分析：对生物钟光同步通路的潜在启示》一文配套数据 * 持久化标识符：数字对象标识符（DOI） * 数据集贡献者：王一帆、Leo W. Beukeboom、Bregje Wertheim、Roelof A. Hut * 数据集引用： > Wang, Y, ### 联系方式 * 联系人姓名：王一帆 * 所属机构：格罗宁根大学进化生命科学研究所进化遗传学研究组 * ORCID标识符：https://orcid.org/0000-0002-6541-7435 * 电子邮箱：[e-mail] * 备用电子邮箱：[e-mail] * 通讯地址：电子邮箱……