Abstract
BackgroundIt is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar.Principal FindingsOn average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon’s diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree.ConclusionsGenome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5′-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.
Highlights
Epigenetic regulation, which is not based on differences in DNA sequence [1,2,3], plays important roles in genome protection, control of gene expression and nuclear inheritance via chromatin structural remodeling and is crucial for promoting phenotypic variation of organisms [4]
Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 59-CCGG methylation level was higher in xylem than in leaves
One powerful and highly stable tool is methylation sensitive amplification polymorphism (MSAP), established based on the amplified fragment length polymorphism (AFLP) [12,13] technique, which was adapted for the analysis of genome-wide sequence-specific methylation status without a priori knowledge of the genome sequence [14,15]
Summary
Epigenetic regulation, which is not based on differences in DNA sequence [1,2,3], plays important roles in genome protection, control of gene expression and nuclear inheritance via chromatin structural remodeling and is crucial for promoting phenotypic variation of organisms [4]. One powerful and highly stable tool is methylation sensitive amplification polymorphism (MSAP), established based on the amplified fragment length polymorphism (AFLP) [12,13] technique, which was adapted for the analysis of genome-wide sequence-specific methylation status without a priori knowledge of the genome sequence [14,15]. Nowadays, this technique is used widely to examine epigenetic variation in plants [12,16,17,18]. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar
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