Stability of environmental DNA methylation and its utility in tracing spawning of fish

The use of environmental DNA (eDNA) as a new method of ecological monitoring is widely applied. Although eDNA can provide important information on the distribution and biomass of particular taxa, an organism’s DNA sequences remain unaltered throughout its existence, which complicates identifying crucial events, including reproduction, with high accuracy. We thus examined DNA methylation as a novel source of information from eDNA, considering that methylation patterns of eggs and sperm released during reproduction differ from those of somatic tissues.
Despite its potential applications, little is known about eDNA methylation, including its stability and methods for detection and quantification. Therefore, we conducted tank experiments and performed methylation analysis targeting 18S rDNA through bisulfite amplicon sequencing.
Methylation of eDNA was not affected by degradation and was equivalent to the rate of genomic DNA from somatic tissues. Unmethylated DNA, which is abundant in the o..., Tank Experiment 1: Monitoring the methylation levels of eDNA undergoing degradation over time
 
In Tank Experiment 1, to examine the methylation levels of eDNA undergoing degradation over time, water samples were collected immediately after the removal of fish from the breeding tanks for up to 72 h. Three breeding tanks (Tank 1-1, Tank 1-2, and Tank 1-3) containing 9 L of water each and one without fish (a blank tank) were prepared (Figure S1). A water sampling tube was installed in the tanks, and the water inlet was covered with a net. A transparent perforated partition board was mounted in the middle of each breeding tank to prevent fluctuations in the eDNA methylation rate caused by sperm and egg release. Six male and six female fish were placed in separate compartments. All tanks were covered with lids, and boards were placed between the tanks to avoid contamination. Fish were fed once a day, ensuring no food was left over, and water temperature was maintained at 27.5 ± 0.5 °C. The ..., , # Data from: Stability of environmental DNA methylation and its utility in tracing spawning of fish

This dataset is supporting information for the submitted manuscript MER-24-0037.R1.

Please refer to the manuscript for information on the equipment, workflows, and materials used.

## Description of the data and file structure

### qPCR data

In the manuscript, section 2.6 of MATERIALS AND METHODS states that the qPCR results for Tank Experiment 1 are found in \"220901_qPCR_ITS2_1_data.csv,\" while the results for Tank Experiment 2 are in \"220901_qPCR_ITS2_2_data.csv,\" \"220901_qPCR_ITS2_3_data.csv,\" and \"220901_qPCR_ITS2_4_data.csv.\"

The \"Well\" column indicates the position on the 96-well plate. The \"Sample Name\" column indicates the template sample. For example, \"Tank1-1-1\"to\"Tank1-1-7\" in \"220901_qPCR_ITS2_1_data.csv\" represent the seven time points of Tank1-1 in Tank experiment 1 in the manuscript, respectively. \"Tank2-1-1\"to\"Tank2-1-16\" in \"220930_qPCR_ITS2_2_data.csv\", \"220930_qPCR_...