Simulated infection induced changes in DNA methylation differ between introduced and native house sparrow (Passer domesticus)

As DNA methylation can change within individuals over time and regulate gene expression, it is important in many aspects of avian biology. It likely plays a critical role in the response of individuals to various stressors, such as infection, environmental change, and the myriad of novel conditions associated with introductions. Here, we use epiRADseq to investigate changes in DNA methylation within-individual birds over eight hours in response to simulated infection. We contrast house sparrows from introduced locations with individuals from native locations, comparing the number of genomic locations that change, their magnitude of change, and the variance among individuals of the change. We detected that introduced individuals change their DNA methylation at more genomic locations, with greater magnitude, and higher variance, compared to native individuals. Together, these findings support a critical role of DNA methylation in an individual’s response to infection, which introduces ind..., We used epiRADseq to screen variation in DNA methylation among house sparrows on the Ion Torrent PGM platform. We followed a genotype-by-sequencing (GBS) protocol developed for the Ion Torrent platform, substituting the DNA methylation-sensitive restriction enzyme HpaII for MspI to construct the epiRADseq library. After restriction digestion, we ligated Ion Torrent IonXpress barcoded adaptors and y-adapters. We ran emulsion polymerase chain reactions following the manufacturers protocols of the Ion PGM-Hi-Q-View OT2-200 kit on the Ion Express OneTouch2 platform. We sequenced resultant fragments following manufacturers protocols of the Ion PGM-Hi-Q-View Sequencing 200 Kit using an Ion 316v2 BC Chips. We demultiplexed runs and conducted quality control with Torrent Suite version 4.4.3. We retained bases above the AQ20 confidence threshold. We trimmed sequences to 100 bp targeting the higher quality sequence at the 5’ end. We performed a de novo assembly and constructed a pseudo-refer..., , # Simulated infection induced changes in DNA methylation differ between introduced and native house sparrow (Passer domesticus)

[https://doi.org/10.5061/dryad.qjq2bvqs2](https://doi.org/10.5061/dryad.qjq2bvqs2)

## Description of the data and file structure

House sparrows were collected from four locations in their native range: Israel (n = 6), Norway (n = 6), Spain (n = 6), and Vietnam (n = 6), and three locations in their introduced range: Australia (n = 3), Canada (n = 6), Senegal (n = 6; Table 1). Upon capture, we took a 50 µl blood sample from the brachial vein of each bird. Immediately after this, we injected each bird with 100 µl of 1 mg/ml-1 lipopolysaccharide in sterile saline subcutaneously over the breast muscle. Post injection, we housed birds individually in wire songbird cages with food and water *ad libitum*. Eight hours post-injection, we took an additional 10 µl of blood from the brachial vein. We extracted DNA samples ending with paired 0- and 8-hour samples for each...,

# 模拟病原感染诱导的DNA甲基化变化在入侵与本土家麻雀（Passer domesticus）间存在显著差异
[https://doi.org/10.5061/dryad.qjq2bvqs2](https://doi.org/10.5061/dryad.qjq2bvqs2)

DNA甲基化（DNA methylation）可随时间在个体内发生动态变化并调控基因表达，因此在鸟类生物学的诸多研究领域中具有核心意义。其极可能在个体应对各类胁迫因子（如病原感染、环境扰动以及物种入侵所伴随的多种新型环境条件）的过程中发挥关键调控作用。本研究利用表观RAD测序（epiRADseq）技术，探究家麻雀（Passer domesticus）在接受模拟病原感染后8小时内的个体内DNA甲基化变化模式。我们对比了入侵分布种群与本土分布种群的家麻雀，比较两组间发生甲基化变化的基因组位点数量、变化幅度以及个体间的变化方差。研究结果显示，与本土种群个体相比，入侵种群个体在更多的基因组位点上发生DNA甲基化变化，且变化幅度更大、个体间变异程度更高。综上，本研究结果支持DNA甲基化在个体应对病原感染过程中发挥关键调控作用的结论，该研究引入了ind……

我们依托离子激流PGM测序平台（Ion Torrent PGM），采用表观RAD测序（epiRADseq）技术对家麻雀群体的DNA甲基化变异进行高通量筛查。本研究遵循针对离子激流平台开发的基因型测序（GBS，genotype-by-sequencing）实验流程，将原流程中的限制性内切酶MspI替换为对DNA甲基化敏感的限制性内切酶HpaII，以此构建表观RAD测序文库。经限制性酶切反应后，我们连接了离子激流IonXpress条形码接头与Y型接头。随后在Ion Express OneTouch2平台上，严格按照Ion PGM-Hi-Q-View OT2-200试剂盒的厂商官方实验方案开展乳液聚合酶链式反应。我们使用Ion 316v2 BC芯片，遵循Ion PGM-Hi-Q-View Sequencing 200试剂盒的厂商官方实验方案对酶切连接后的目标片段进行高通量测序。我们通过Torrent Suite版本4.4.3（Torrent Suite v4.4.3）对原始测序数据进行拆分与质量控制，保留AQ20置信阈值以上的有效碱基，并将序列修剪至100 bp，以保留5'端的高质量测序序列。我们开展了从头组装（de novo assembly）并构建了伪参考基因组pseudo-refer……

## 数据与文件结构说明
我们从家麻雀的本土自然分布区采集了4个种群的样本：以色列（n=6）、挪威（n=6）、西班牙（n=6）以及越南（n=6），同时从其入侵分布区采集了3个种群的样本：澳大利亚（n=3）、加拿大（n=6）以及塞内加尔（n=6；详见表1）。捕获个体后，我们从每只实验鸟的臂静脉采集50 µl的血液样本作为初始（0小时）样品。采血后立即对每只鸟的胸肌部位进行皮下注射，注射剂量为100 µl浓度为1 mg·ml⁻¹的脂多糖无菌生理盐水溶液。注射完成后，我们将每只实验鸟单独饲养于金属鸣禽专用笼中，提供充足的食物与饮用水以供自由采食饮用。注射后8小时，我们再次从每只鸟的臂静脉采集10 µl的血液样本作为终点（8小时）样品。我们提取了所有个体的0小时与8小时成对血液样本的基因组DNA，用于后续实验分析……