ONT whole-genome DNA methylation, direct RNA methylation, and Hi-C sequencing of Oryza sativa
DNA methylation (5mC and 6mA) and RNA methylation (m5C and m6A) are important epigenetic modifications involved in the regulation of gene expression and chromatin structure in plants. In this study, we employed Oxford Nanopore Technologies (ONT) long-read sequencing and Illumina Hi-C sequencing to generate multi-omics datasets for Oryza sativa. For DNA methylation, we performed ONT whole-genome sequencing on leaf tissue with two biological replicates (NIBP1 and NIBP2), using Guppy for basecalling and Tombo v1.5 with the alternative model to detect 5mC and 6mA sites, including hyper-methylated fractions. For RNA methylation, we conducted ONT direct RNA sequencing on mixed tissues (root, stem, and leaf), combined with Illumina NGS data for quality control. We identified m5C and m6A modifications using Tombo v1.5 and nanom6A, with a statistical threshold of |statistic| > 2.5 for m5C. Additionally, we performed Hi-C sequencing on leaf tissue using the Illumina platform to investigate chromatin conformation, generating valid paired-end pairs for three-dimensional genome analysis. The resulting datasets include raw sequencing reads, methylation site calls (all and hyper-methylated fractions for 5mC, 6mA, and CpG), full-length transcript assemblies, and Hi-C interaction matrices. These data provide a resource for studying the relationships among DNA methylation, RNA methylation, and chromatin organization in rice, and may support future epigenetic research in cereal crops.