Genome-wide methylation profiling data for diploid crabapple HCT-DP and its autotetraploid HCT-TP leaves at 40 days after in vitro culture

The raw sequencing reads (FASTQ files) from this study are unfortunately no longer available due to an unforeseen archive error. As an alternative, we deposite the processed single-base methylation data supporting the findings of this study in the ZenodoThis dataset contains genome-wide, single-base resolution DNA methylation calls for diploid crabapple (Malus spp.) cultivar 'HCT-DP' and its corresponding autotetraploid line 'HCT-TP'. Seedlings of both genotypes were harvested 40 days after in vitro culture, with three biological replicates per genotype (HCT-DP: replicates 1–3; HCT-TP: replicates 1–3), totaling six samples. For each replicate sample, all methylation call files are provided as a compressed archive (.zip) containing three tab-delimited text (.txt) files classified by sequence context: *_CG.txt: methylation at CG sites *_CHG.txt: methylation at CHG sites (H = A, C, or T) *_CHH.txt: methylation at CHH sites (H = A, C, or T) Each .txt file includes the following columns: unique site identifier (chrBase), chromosome name (chr), genomic coordinate (base, 1-based coordinates), strand (strand), read coverage depth (coverage), percentage of methylated cytosines (freqC), and percentage of unmethylated cytosines (freqT). These data allow for direct calculation of methylation levels and coverage-based filtering for downstream analyses. File naming convention: [Genotype]_[Replicate].Original_Meth_Site.zip (e.g., HCT_DP_1.Original_Meth_Site.zip). Each archive contains three files named as [Genotype]_[Replicate]_[Context].txt (e.g., HCT_DP_1_CG.txt).