Highly and lowly domesticated endangered fish from a conservation hatchery diverge in their thermal physiology, transcriptome, and methylome

We investigated whether elevated rearing temperature through larval development of Delta smelt adjusted upper thermal tolerance limits (acclimation) in Delta Smelt, whether upper thermal tolerance and plasticity (acclimation ability) differed between fish with old or recent hatchery ancestry (high or low domestication index; DI), and temperature and DI effects on liver transcriptome and methylome patterns. This dataset contains global methylation levels from CpG count matrices for every 100 individuals, generated using the program Bismark. Each file corresponds to a single individual fish. Within each file is a matrix of loci (chromosomal and SNP location in the Delta smelt genome) and whether the site is methylated or not. The file identification corresponds to the fish ID. Metadata for the fish (including treatment conditions) is found in the file:&nbsp;methyl_metadata.xlsx. All procedures were approved by the UC Davis Institutional Animal Care and Use Committee (IACUC Protocol #21915..., We reared Delta Smelt from embryos until&nbsp;143-151 dpf at either 15 °C or 18 °C. We then dissected livers and flash-froze them. We performed whole-genome bisulfite sequencing on ~100 livers. We used the program Bismark to create CpG site matrix files for each individual. These files were used as input in the DMRichR package to look for differential methylation patterns. , <br /> # Data from: Highly and lowly domesticated endangered fish from a conservation hatchery diverge in their thermal physiology, transcriptome, and methylome Dataset DOI: [10.5061/dryad.j9kd51ctj](https://doi.org/10.5061/dryad.j9kd51ctj) ## Description of the data and file structure Each file corresponds to an individual fish (treatment conditions for each fish are located in methyl_metadata.xlsx). Each file is a tabular count matrix of methylated sites. Column 1: Chromosome number Column 2: genomic position Column 3: methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-) Column 4: read counts methylated Column 5: read counts unmethylated Column 6: Output discriminates between cytosine methylation in `CpG`, `CHG` and `CHH` context Column 7: The specific 3-base sequence context <br /> Within the methyl_metadata.xlsx there are 5 columns: Column 1: Fish ID that corresponds to each CpG_report file. Column 2: full treatment description (..., ,本研究旨在探究：三角洲银汉鱼（Delta smelt）幼体发育阶段升高的饲养温度是否会调整其高温耐受极限（驯化作用）；具有古老或近期孵化场血统且驯化指数（domestication index, DI）为高或低的个体之间，高温耐受性及其可塑性（驯化能力）是否存在差异；以及温度与驯化指数对肝脏转录组与甲基化组模式的影响。本数据集包含约100尾个体的CpG计数矩阵对应的全基因组甲基化水平，通过Bismark软件生成。每个文件对应一尾试验用鱼，文件内包含位点矩阵（涵盖三角洲银汉鱼基因组中的染色体位置与单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点）以及该位点是否发生甲基化的信息，文件命名与试验鱼ID一一对应。试验鱼的元数据（包含处理条件）可在文件"methyl_metadata.xlsx"中获取。所有实验操作均经加州大学戴维斯分校实验动物护理与使用委员会（Institutional Animal Care and Use Committee, IACUC）审批（协议编号#21915...）。 我们将三角洲银汉鱼的胚胎饲养至受精后143~151天（days post fertilization, dpf），饲养温度分别设置为15℃与18℃。随后解剖其肝脏并快速冷冻，对约100尾鱼的肝脏开展全基因组亚硫酸氢盐测序。使用Bismark软件为每个个体生成CpG位点计数矩阵文件，将这些文件作为DMRichR软件包的输入，以分析差异甲基化模式。 # 数据来源：《保护孵化场中高、低驯化程度的濒危鱼类在热生理、转录组与甲基化组上存在分化》 数据集DOI: [10.5061/dryad.j9kd51ctj](https://doi.org/10.5061/dryad.j9kd51ctj) ## 数据与文件结构说明 每个文件对应一尾试验鱼（每尾鱼的处理条件详见"methyl_metadata.xlsx"）。每个文件为甲基化位点的表格计数矩阵： 1. 第1列：染色体编号 2. 第2列：基因组位置 3. 第3列：甲基化的胞嘧啶标记为正向链（+），未甲基化的胞嘧啶标记为反向链（-） 4. 第4列：甲基化reads计数 5. 第5列：未甲基化reads计数 6. 第6列：输出结果区分`CpG`、`CHG`与`CHH`三种胞嘧啶甲基化语境 7. 第7列：具体的3碱基序列语境 在"methyl_metadata.xlsx"文件中包含5列信息： 1. 第1列：与每个`CpG_report`文件对应的试验鱼ID 2. 第2列：完整处理条件描述