DOI: 10.5061/dryad.nk98sf7zk
title: DNA methylation data for Atlantic herring (2020)

description: Understanding the molecular mechanisms underlying individual responses to
 environmental changes is crucial for species conservation and management.
 Pelagic fishes including Atlantic herring (Clupea harengus) are of
 particular interest because of their key ecological and economic roles and
 their susceptibility to a changing ocean from global warming. Temperature
 and photoperiod have been linked with spawning time and location in adult
 herring, but no study has thus far investigated the role of environmental
 factors on gene regulation during the vulnerable early developmental
 stages. Here we examine DNA methylation patterns of larval herring bred
 under two temperatures (11°C and 13°C) and photoperiod (6 hr and 12 hr)
 regimes in a 2X2 factorial design. We found consistently high levels of
 global methylation across all individuals and a decline in global
 methylation with increased developmental stage that was more pronounced at
 13°C (P ≤ 0.007) than at 11°C (P ≥ 0.21). Most of the differentially
 methylated sites were in exon and promoter regions for genes linked to
 metabolism and development, some of which were hypermethylated at higher
 temperature. These results demonstrate the important role of DNA
 methylation during larval development and suggest that this molecular
 mechanism might be key in regulating early-stage responses to
 environmental stressors in Atlantic herring.
description: DNA from 53 Atlantic herring
 larvae (22 from 2019 and 32 from 2020) from different temperatures (11 and
 13°C) and photoperiod (6h and 12h)
 treatments were sent for whole genome bisulfite sequencing
 (details in paper). Bisulfite conversion was done using NEBNext
 Ultra II Library Prep Kit for Illumina workflow (New England BioLabs,
 Oshawa, Canada) and sequencing was conducted on Illumina’s NovaSeq 6000
 PE150 at 49X coverage. These are the raw sequencing reads that we use for
 downstream analyses.
description: Post processing include quality control of reads using FastQC
 v0.11.5 (Andrews, 2020) and trimming was done using Trimmomatic (Bolger et
 al., 2014). Alignment to <em>Clupea harengus </em>reference
 genome (GCF_900700415.1_Ch_v2.0.2, NCBI) was done using Bismark v0.22.3
 (Krueger and Andrews, 2011) and Bowtie2 v2.4.1 (Langmead and Salzberg,
 2012) with default settings. Differential methylation analysis was done
 in <em>methylKit </em>(Akalin et al., 2012).
description: # DNA methylation data\_Atlanticherring(2020)
 [https://doi.org/10.5061/dryad.nk98sf7zk](https://doi.org/10.5061/dryad.nk98sf7zk) ## Description of the data and file structure DNA from 53 Atlantic herring larvae (22 from 2019 and 32 from 2020) from different temperature (11 and 13°C) and photoperiod (6h and 12h) treatments were sent for whole genome bisulfite sequencing (details in paper). Bisulfite conversion was done using NEBNext Ultra II Library Prep Kit for Illumina workflow (New England BioLabs, Oshawa, Canada) and sequencing was conducted on Illumina’s NovaSeq 6000 PE150 at 49X coverage. These are the raw sequencing reads that we use for downstream analyses.   Post processing include quality control of reads using FastQC v0.11.5 (Andrews, 2020) and trimming was done using Trimmomatic (Bolger et al., 2014). Alignment to *Clupea harengus* reference genome (GCF\_900700415.1\_Ch\_v2.0.2, NCBI) was done using Bismark v0.22.3 (Krueger and Andrews, 2011) and Bowtie2 v2.4.1 (Langmead and Salzberg, 2012) with default settings. Differential methylation analysis was done in *methylKit* (Akalin et al., 2012). **Note: Currently uploaded files are only for the 32 herring from 2020 in sorted.bam format.** The treatments are shown below (Modified from Table S2 in the original manuscript): **Table S2A.** List of 32 Atlantic herring larvae sampled in 2020 from the reciprocal transplant experiment conducted in the Aquatron with the sample ID, raceway ID (Raceway), development time (Time), temperature treatment (Temp), and photoperiod treatment (Photoperiod). All samples were stored in 95% Ethanol tubes. Individuals that are greyed out did not pass the initial quality control post extraction and were not sent for sequencing. In total, 32 individuals were sent for sequencing. BR: Bottom Right, TR: Top Right, BL: Bottom Left, TL: Top Left. | Number | Sample ID | Raceway | Time | Temp | Photoperiod | | ------ | --------- | ------- | ---- | ---- | ----------- | | 1 | 5B | BL | 1 | 13 | 6:18 | | 2 | 1C | BL | 1 | 13 | 6:18 | | 3 | 2B | BL | 1 | 13 | 6:18 | | 4 | 5B | BL | 2 | 13 | 6:18 | | 5 | 4C | BL | 2 | 13 | 6:18 | | 6 | 3B | BL | 2 | 13 | 6:18 | | 10 | 6 | TL | 1 | 13 | 12:12 | | 11 | 4 | TL | 1 | 13 | 12:12 | | 12 | 7C | TL | 1 | 13 | 12:12 | | 13 | 5B | TL | 2 | 13 | 12:12 | | 14 | 4 | TL | 2 | 13 | 12:12 | | 15 | 7C | TL | 2 | 13 | 12:12 | | 22 | 4 | BR | 2 | 11 | 6:18 | | 23 | 4B | BR | 2 | 11 | 6:18 | | 24 | 3C | BR | 2 | 11 | 6:18 | | 27 | 2B | BR | 3 | 11 | 6:18 | | 28 | 2 | TR | 1 | 11 | 12:12 | | 29 | 4C | TR | 1 | 11 | 12:12 | | 30 | 8C | TR | 1 | 11 | 12:12 | | 31 | 5 | TR | 2 | 11 | 12:12 | | 32 | 3B | TR | 2 | 11 | 12:12 | | 33 | 6C | TR | 2 | 11 | 12:12 | | 42 | 7 | BL | 1 | 13 | 6:18 | | 43 | 8C | TL | 3 | 13 | 12:12 | | 45 | 6B | TL | 3 | 13 | 12:12 | | 46 | 2 | BR | 3 | 11 | 6:18 | | 47 | 4 | BR | 3 | 11 | 6:18 | | 49 | 3 | TR | 3 | 11 | 12:12 | | 50 | 6 | TR | 3 | 11 | 12:12 | | 55 | 7B | TR | 3 | 11 | 12:12 | | 1A | 1C\* | BL | 1 | 13 | 6:18 | | 2A | 7 | TL | 3 | 13 | 12:12 | ## Code/Software An example annotated pipeline for processing the data in *methylKit* can be found on Github repository: ([https://github.com/jforce92/HerringMethylation.git](https://github.com/jforce92/HerringMethylation.git)).