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Int. J. Mol. Sci. 2014, 15(12), 22874-22886; doi:10.3390/ijms151222874

Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning

1,†,* , 1,†
,
1,†
,
1
and
1,2,*
1
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
2
Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Beijing Road, Urumqi 830011, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 25 October 2014 / Revised: 27 November 2014 / Accepted: 1 December 2014 / Published: 10 December 2014
(This article belongs to the Special Issue Plant Molecular Biology)
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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. View Full-Text
Keywords: Betula platyphylla; plant; epigenetic; DNA methylation; BS-Seq Betula platyphylla; plant; epigenetic; DNA methylation; BS-Seq
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Su, C.; Wang, C.; He, L.; Yang, C.; Wang, Y. Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning. Int. J. Mol. Sci. 2014, 15, 22874-22886.

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