Pesticide and pathogen exposure causes idiosyncratic gene expression responses across four diverse North American bumble bee species

Bumble bee populations of certain species have been declining precipitously in North America over several decades. Hypotheses for declines include exposure to the fungal pathogen Nosema bombi and neonicotinoid pesticides. Importantly, populations of some bumble bee species remain stable despite their presumed exposure to these same stressors. Here we hypothesize that declining and stable species, respectively, exhibit distinct responses to N. bombi and neonicotinoid pesticides, detectable as differential gene expression profiles. To test this, we exposed developing larvae from colonies of Bombus occidentalis (declining) and B. impatiens (stable) to N. bombi and to the neonicotinoid imidacloprid, plus a combination of both. RNA-seq analysis revealed almost no overlap between these species in gene expression responses to the individual stressors. Combined-stressor effects were more similar, but nevertheless differed significantly in differentially expressed genes and in gene coexpression ..., Experimental design
Colonies from four North American bumble bee species were set in the Illinois State University facilities: Bombus impatiens (n = 7), Bombus occidentalis (n = 3), Bombus griseocollis (n = 4) and Bombus terricola (n = 2). Four microcolonies consisting of five adult workers and a larval brood clump were set from each parental colony. Each set of microcolonies from a source colony was exposed to one of four possible treatments:

unexposed to imidacloprid and N. bombi (control)
exposed to N. bombi, unexposed to imidacloprid
exposed to imidacloprid, unexposed to N. bombi

exposed to both imidacloprid and N. bombi

After 24 h of provisioning the microcolonies with untreated sugar water and pollen ad libitum, both were replaced with either control or imidacloprid (7 ppb) treated provisions for 72 h. After the first exposure event, provisions were again switched to untreated, and larvae were individually fed a 2 μL inoculum of either control or Nosema bombi (20,000 spore..., , # Data from: Diverse bumble bee species exhibit idiosyncratic gene expression responses to pathogens and pesticides

[https://doi.org/10.5061/dryad.rxwdbrvjv](https://doi.org/10.5061/dryad.rxwdbrvjv)

## Description of the data and file structure

There are a total of four datasets and eleven scripts available from this resource.

Datasets \"data_raw_read_counts.csv\" and \"data_module_eigenvalues.csv\" can be generated following the RNA-seq pipeline; \"adapters.fa\" can be provided by sequencing services; \"data_qpcr_rqs.csv\" was processed from raw data generated from the thermocycler used for the analysis.

Bash scripts (script numbers 00 to 06) are automated and can be run from a Linux OS prompt, but some modifications are to be made before running the scripts, besides installing program and library dependencies. R scripts (script numbers 07 to 10) are to be run in an R environment line by line in a prompt with active R environment or in a R GUI (such as Rstudio), running Rscript won't work...,

北美地区部分物种的熊蜂种群在过去数十年间急剧下降。目前提出的种群衰退假说包括暴露于真菌病原体熊蜂微孢子虫（Nosema bombi）以及新烟碱类杀虫剂。值得注意的是，尽管部分熊蜂物种被认为同样暴露于这些胁迫因子，其种群却保持稳定。本研究提出假说：衰退种群与稳定种群分别对熊蜂微孢子虫和新烟碱类杀虫剂呈现差异化响应，这种响应可通过差异基因表达谱加以区分。为验证该假说，我们将西方熊蜂（Bombus occidentalis，衰退种群）与普通熊蜂（Bombus impatiens，稳定种群）的发育幼虫分别暴露于熊蜂微孢子虫、新烟碱类杀虫剂吡虫啉（imidacloprid），以及二者联合处理组。RNA测序（RNA-seq）分析显示，这两个物种在单一胁迫因子下的基因表达响应几乎无重叠。联合胁迫的效应虽更为相似，但在差异表达基因与基因共表达……方面仍存在显著差异。

## 实验设计
本研究在伊利诺伊州立大学设施内构建了四种北美熊蜂的蜂群：普通熊蜂（Bombus impatiens，n = 7）、西方熊蜂（Bombus occidentalis，n = 3）、灰领熊蜂（Bombus griseocollis，n = 4）以及林地熊蜂（Bombus terricola，n = 2）。从每个亲本蜂群中构建4个微蜂群，每个微蜂群包含5只成年工蜂与一团幼虫巢脾。来自同一亲本蜂群的微蜂群分别接受4种处理之一：

1. 未暴露于吡虫啉与熊蜂微孢子虫（对照组）
2. 暴露于熊蜂微孢子虫，未暴露于吡虫啉
3. 暴露于吡虫啉，未暴露于熊蜂微孢子虫
4. 同时暴露于吡虫啉与熊蜂微孢子虫

先为微蜂群提供未处理的糖水与花粉自由采食24小时后，将其替换为对照组或含7 ppb吡虫啉的处理饲料，持续72小时。首次暴露结束后，再次将饲料换回未处理状态，随后分别向每头幼虫接种2 μL的对照溶液或熊蜂微孢子虫孢子液（20,000孢子……）

# 数据来自：多样的熊蜂物种对病原体与杀虫剂呈现特异性基因表达响应
[https://doi.org/10.5061/dryad.rxwdbrvjv]

## 数据与文件结构说明
本资源共包含4份数据集与11份脚本。
数据集"data_raw_read_counts.csv"与"data_module_eigenvalues.csv"可通过RNA测序（RNA-seq）分析流程生成；"adapters.fa"可由测序服务机构提供；"data_qpcr_rqs.csv"由本研究使用的定量PCR热循环仪生成的原始数据处理得到。
Bash脚本（脚本编号00至06）为自动化脚本，可在Linux操作系统命令行运行，但在运行前除需安装程序与库依赖外，还需对脚本进行部分修改。R脚本（脚本编号07至10）需在激活的R环境命令行或R图形用户界面（如RStudio）中逐行运行，直接运行Rscript命令无法正常执行。