Data availability
The pipeline scripts used for this study are available at: https://github.com/thomasvangurp/epiGBS, with a bug‐fix modification (https://github.com/MWSchmid/epiGBS_Nov_2017_fixed). The raw sequence data files for epiGBS (Illumina paired end reads), and for RNAseq (individual samples’ Illumina paired end reads after quality trimming) have been submitted to the Sequence Read Archive (SRA) of NCBI under project number PRJNA790924. The barcodes (barcodes.tsv) required to process the raw epiGBS sequencing data available on SRA, the reference contigs (de_novo_contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the de novo transcriptome assembly (de_novo_transcriptome.fasta.gz) are available on zenodo (doi: 10.5281/zenodo.5776915).