DNA methylation plays a critical role in the regulation of gene expression. Most 
studies of DNA methylation have been performed in herbaceous plants, and little 
is known about the methylation patterns in tree genomes. In the present study, 
we generated a map of methylated cytosines at single base pair resolution for 
Betula platyphylla (white birch) by bisulfite sequencing combined with 
transcriptomics to analyze DNA methylation and its effects on gene expression. 
We obtained a detailed view of the function of DNA methylation sequence 
composition and distribution in the genome of B. platyphylla. There are 34,460 
genes in the whole genome of birch, and 31,297 genes are methylated. 
Conservatively, we estimated that 14.29% of genomic cytosines are 
methylcytosines in birch. Among the methylation sites, the CHH context accounts 
for 48.86%, and is the largest proportion. Combined transcriptome and 
methylation analysis showed that the genes with moderate methylation levels had 
higher expression levels than genes with high and low methylation. In addition, 
methylated genes are highly enriched for the GO subcategories of binding 
activities, catalytic activities, cellular processes, response to stimulus and 
cell death, suggesting that methylation mediates these pathways in birch trees.