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Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology

DNA methylation is critical to the regulation of transposable elements and gene expression. Traditional methods of methylation quantification rely on bisulfite conversion, which requires treatments to the DNA that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (65x nanopore and 111X Illumina) and Acer saccharum (93x nanopore and 148X Illumina). The nanopore reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and the new hybrid assemblies to generate four epigenomes. The abundance and distribution of genes (including those previously associated with abiotic stress response), repeats, and methylation contexts were examined and compared with those of recently characterized broadleaf tree species.