Shotgun Bisulfite Sequencing Of The Betula Platyphylla Genome Reveals The Tree’s DNA Methylation Patterning

DNA methylation is one of the earliest discovered DNA modification methods, it can change the conformation of DNA, chromatin structure, DNA stability, and it also affects interactions between DNA and protein. Thereby this DNA methylation modified approach can affect gene expression, maintaining genome stability, control of imprinted genes, and plays an important role in Hybrid. However, 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.In different functional genomic elements of birch genome, transposable elements (TE) has the highest methylation level. We further calculated methylation levels in the context of gene bodies and 2 kb of their upstream and downstream regions, and TEs and 0.5 kb of their upstream and downstream regions. This trend of methylation level was similar to that of Arabidopsis thaliana, Populus trichocarpa, Japonica and Oryza sativa, and the trend may be a common characteristic of flowering plants. We also found that methylation level in introns was higher than in exons, which is opposite to A. thaliana, P. trichocarp, and O. sativa. This high enrichment of methylation in introns may have a direct or indirect role in the regulation of transcription in birch. However, there is no correlation between sequence context and methylation preference in birch.For exploring the relationship between DNA methylation level and gene transcription in Betula, we generate transcriptome sequencing, using the same plant material with birch methylation sequencing.9544572900 nt data were generated, and 43,210 Unigenes were assembled. N50 of Unigenes have reached 1705 nt. The correlation between two biological replicates have reached 0.976. 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.