DOI: 10.5061/dryad.z34tmpgqd
title: Data from: Epigenomic changes in Ostrinia moths under elevated pupal and adult temperature

description: Epigenetic changes in methylation of DNA may occur in response to
 environmental stressors, including warming climates. DNA methylation may
 also play an important role in regulating gene expression during both male
 and female reproduction in many insect species. ­­­­­However, it is
 currently unknown how DNA methylation shifts when individuals are
 reproducing under warmer temperatures. We exposed European corn borer
 moths (Ostrinia nubilalis) to heat during the pupal and adult life stages
 then investigated changes in DNA methylation across the genome using
 enzymatic methyl-seq (EM-seq). We compared methylation patterns in
 reproductive males and females exposed to heat (28°C) to those that
 experienced an ambient temperature (23°C). We found that heat exposure led
 to a small but significant increase in the percentage of methylated CpG
 sites throughout the genome in both sexes. However, DNA methylation rates
 were higher in females and differential methylation following heat
 exposure localized to unique regions in each sex. In males, methylation
 shifted within genes belonging to pathways including Hippo signaling,
 ubiquitin mediated proteolysis, DNA damage repair, and spermatogenesis. In
 females, differential methylation occurred in genes related to histone
 modification and oogenesis. Our results suggest that DNA methylation
 patterns respond to a moderate heat exposure in Lepidoptera and provide
 insight into epigenetic responses to heatwaves, suggesting novel pathways
 that may be involved in responding to heat stress during metamorphosis and
 reproduction.
description: Enzymatic methyl-seq from <em>Ostrinia
 nubilalis </em>analyzed using Bwa-meth, MethylDackel, BSSeq (R
 package) and methylSig (R package) software were used. Pipeline available
 on GitHub: https://github.com/gmkozak/Methylation-Pipeline
description: # Epigenomic changes in Ostrinia moths under elevated pupal and adult
 temperature
 [https://doi.org/10.5061/dryad.z34tmpgqd](https://doi.org/10.5061/dryad.z34tmpgqd) ## Description of the data and file structure Enzymatic methyl-seq from Ostrinia nubilalis following pipeline available on GitHub: [https://github.com/gmkozak/Methylation-Pipeline](https://github.com/gmkozak/Methylation-Pipeline) Bwa-meth, MethylDackel, BSSeq (R package), and methylSig (R package) software were used to determine differentially methylated regions (DMRs). Analysis was done using CpG methylation sites summed within non-overlapping windows with a width of 100bp. One analysis used Biscuit rather than Bwa-meth to call methylation. ### Files and variables #### File: Male.Significant.DMRs.List.csv **Description:** Significant Male DMRs (Heat vs. Control). Using 7 males per exposure, bwa-meth pipeline. Significant DMRs had q&lt;0.05 and meth_diff&gt;10. NAs indicate DMRs that lack gene names in Ostrinia nubilalis or Drosophila melanogaster. ##### Variables * Scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp: Window Position End Scaffold in bp * meth_H: Methylation in Heat (within sex) * meth_L: Methylation in Control/Low Temp (within sex) * meth_diff: meth_H - meth_L * direction: methylation bias (H=heat, L=control/low temp) * stat: Z score for methylation bias * p-value: raw p-value * FDR q-value: False Discovery Rate (FDR) corrected q-value * GeneID: Ostrinia nubilalis Gene ID (ostnu) * GeneDescription: Gene name in Genome * Position: DMR Location in Gene (Exon, Intron, UTR) * DroMelName: Drosophila melanogaster Gene Name * DroMelSymbol: Drosophila melanogaster Gene Symbol * Unique: Unique Gene or Location #### File: Female.Significant.DMRs.List.csv **Description:**  Significant Female DMRs (Heat vs. Control)**.** Using 7 females in heat and 5 females in control, bwa-meth pipeline. Significant DMRs had q&lt;0.05 and meth_diff&gt;10. NAs indicate DMRs that lack gene names in Ostrinia nubilalis or Drosophila melanogaster. ##### Variables * Scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp:Window Position End Scaffold in bp * meth_H: Methylation in Heat (within sex) * meth_L: Methylation in Control/Low Temp (within sex) * meth_diff: meth_H - meth_L * direction: methylation bias (H=heat, L=control/low temp) * stat: Z score for methylation bias * p-value: raw p-value * FDR q-value: False Discovery Rate (FDR) corrected q-value * GeneID: Ostrinia nubilalis Gene ID (ostnu) * GeneDescription: Gene name in Genome * Position: DMR Location in Gene (Exon, Intron, UTR) * DroMelName: Drosophila melanogaster Gene Name * DroMelSymbol: Drosophila melanogaster Gene Symbol * Unique: Unique Gene or Location #### File: Between.Sex.Significant.DMRs.csv **Description:**  Significant Male vs. Female DMRs (Heat or Control). Using 7 females and 7males in heat; 7 males and 5 females in control. Significant DMRs had q&lt;0.05 and meth_diff&gt;10.Analyzed with bwa-meth pipeline. NAs indicate DMRs that lack gene names in Ostrinia nubilalis or Drosophila melanogaster. Variables * Exposure: Heat or Control * Scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp:Window Position End Scaffold in bp * meth_M: Methylation in Males * meth_F: Methylation in Females * meth_diff: meth_M- meth_F * direction: methylation bias (M=male, F=female) * stat: Z score for methylation bias * p-value: raw p-value * FDR q-value: False Discovery Rate (FDR) corrected q-value * GeneID: Ostrinia nubilalis Gene ID (ostnu) * GeneDescription: Gene name in Genome * Position: DMR Location in Gene (Exon, Intron, UTR) * DroMelName: Drosophila melanogaster Gene Name * DroMelSymbol: Drosophila melanogaster Gene Symbol * Unique: Unique Gene or Location #### File: Control\_MvF\_4\_7\_fdr2R.csv **Description:** All DMRs Control Males vs. Females. All DMRs that had methylation with sequencing coverage above 10 in at least 4 individuals per sex. 7 males and 5 females in control. Analyzed with bwa-meth pipeline. ##### Variables * scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp: Window Position End Scaffold in bp * meth_case: Methylation in Heat (within sex) or Males (between sex) * meth_control: Methylation in Control (within sex) or Females (between sex) * meth_diff: meth_case - meth_control * direction: methylation bias (M=male, F=female) * stat: Z score for methylation bias * pvalue: raw p-value * fdr: False Discovery Rate (FDR) corrected q-value (FDR q-value) #### File: Female\_CvH\_4\_7\_zerorem\_fdrR2.csv **Description:** All DMRs Females Heat vs. Control. All DMRs that had methylation with sequencing coverage above 10 in at least 4 individuals per sex. 7 females in heat and 5 females in control. Analyzed with bwa-meth pipeline. ##### Variables * scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp: Window Position End Scaffold in bp * meth_case: Methylation in Heat (within sex) or Males (between sex) * meth_control: Methylation in Control (within sex) or Females (between sex) * meth_diff: meth_case - meth_control * direction: Methylation Bias * stat: Z score for methylation bias * pvalue: raw p-value * fdr: False Discovery Rate (FDR) corrected q-value (FDR q-value) #### File: Heat\_MvF\_4\_7\_fdr2R.csv **Description:** All DMRs Heat Males vs. Females. All DMRs that had methylation with sequencing coverage above 10 in at least 4 individuals per exposure per sex. 7 males and 7 females. Analyzed with bwa-meth pipeline. ##### Variables * scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp: Window Position End Scaffold in bp * meth_case: Methylation in Heat (within sex) or Males (between sex) * meth_control: Methylation in Control (within sex) or Females (between sex) * meth_diff: meth_case - meth_control * direction: methylation bias (M=male, F=female) * stat: Z score for methylation bias * pvalue: raw p-value * fdr: False Discovery Rate (FDR) corrected q-value (FDR q-value) #### File: Male\_CvH\_4\_7\_zerorem\_fdrR.csv **Description:** All DMRs Males Heat vs. Control (7 males). All DMRs that had methylation with sequencing coverage above 10 in at least 4 individuals per exposure. 7 males in heat and 7 males in control. Analyzed with bwa-meth pipeline. ##### Variables * scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp: Window Position End Scaffold in bp * meth_case: Methylation in Heat (within sex) or Males (between sex) * meth_control: Methylation in Control (within sex) or Females (between sex) * meth_diff: meth_case - meth_control * direction: methylation bias (H=heat, L=control/low temp) * stat: Z score for methylation bias * pvalue: raw p-value * fdr: False Discovery Rate (FDR) corrected q-value (FDR q-value) #### File: Male.Significant.Biscuit.fdrR.csv **Description:**  Significant DMRs Males (Heat vs. Control). Using 7 males per exposure, Biscuit pipeline. Significant DMRs had q&lt;0.05 and meth_diff&gt;10. for DMRs that had methylation with sequencing coverage above 10 in at least 4 individuals per exposure. ##### Variables * scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp: Window Position End Scaffold in bp * meth_case: Methylation in Heat (within sex) or Males (between sex) * meth_control: Methylation in Control (within sex) or Females (between sex) * meth_diff: meth_case - meth_control * direction: methylation bias (H=heat, L=control/low temp) * stat: Z score for methylation bias * pvalue: raw p-value * fdr: False Discovery Rate (FDR) corrected q-value (FDR q-value) #### File: Male.Significant.Only3.fdrR.csv **Description:** Significant DMRs (Heat vs. Control). Using only 3 males per exposure, bwa-meth pipeline. Significant DMRs had q&lt;0.05 and meth_diff&gt;10. for DMRs that had methylation with sequencing coverage above 10 in at least 2 individuals per exposure. ##### Variables * scaffold: Ostrinia nubilalis Genome scaffold number (Genbank BioProject PRJNA534504) * start.bp: Window Position Start Scaffold in bp * end.bp: Window Position End Scaffold in bp * meth_case: Methylation in Heat (within sex) or Males (between sex) * meth_control: Methylation in Control (within sex) or Females (between sex) * meth_diff: meth_case - meth_control * direction: methylation bias (H=heat, L=control/low temp) * stat: Z score for methylation bias * pvalue: raw p-value * fdr: False Discovery Rate (FDR) corrected q-value (FDR q-value)