title: Shotgun bisulfite sequencing of the Betula platyphylla genome reveals the tree's DNA methylation patterning.
abstract: 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.
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China. changsu1989@gmail.com.
authors.forename: Chang
authors.initials: C
authors.lastname: Su
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China. wangchao7993@126.com.
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China. helin8565@126.com.
authors.forename: Lin
authors.initials: L
authors.lastname: He
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China. yangcp@nefu.edu.cn.
authors.forename: Chuanping
authors.initials: C
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China. wangyucheng@ms.xjb.ac.cn.
authors.forename: Yucheng
authors.initials: Y
authors.lastname: Wang
mesh_terms: D029662:Betula / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D004251:DNA Transposable Elements; D044127:Epigenesis, Genetic; D005091:Exons; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics; D007438:Introns; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements