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Genes 2018, 9(12), 602; https://doi.org/10.3390/genes9120602

DNA Methylation Diversification at the Integrated Organellar DNA-Like Sequence

1
Faculty of Life Science, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
2
Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
3
Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
4
Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
*
Author to whom correspondence should be addressed.
Received: 15 October 2018 / Revised: 20 November 2018 / Accepted: 28 November 2018 / Published: 3 December 2018
(This article belongs to the Special Issue Transgenerational Epigenetics in Plants)
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Abstract

Plants have a lot of diversity in epigenetic modifications such as DNA methylation in their natural populations or cultivars. Although many studies observing the epigenetic diversity within and among species have been reported, the mechanisms how these variations are generated are still not clear. In addition to the de novo spontaneous epi-mutation, the intra- and inter-specific crossing can also cause a change of epigenetic modifications in their progenies. Here we report an example of diversification of DNA methylation by crossing and succeeding selfing. We traced the inheritance pattern of epigenetic modification during the crossing experiment between two natural strains Columbia (Col), and Landsberg electa (Ler) in model plant Arabidopsis thaliana to observe the inheritance of DNA methylation in two organellar DNA-like sequence regions in the nuclear genome. Because organellar DNA integration to the nuclear genome is common in flowering plants and these sequences are occasionally methylated, such DNA could be the novel source of plant genome evolution. The amplicon sequencing, using bisulfite-converted DNA and a next-generation auto-sequencer, was able to efficiently track the heredity of DNA methylation in F1 and F2 populations. One region showed hypomethylation in the F1 population and succeeding elevation of DNA methylation with large variance in the F2 population. The methylation level of Col and Ler alleles in F2 heterozygotes showed a significant positive correlation, implying the trans-chromosomal effect on DNA methylation. The results may suggest the possible mechanism causing the natural epigenetic diversity within plant populations. View Full-Text
Keywords: DNA methylation; amplicon sequencing; NUMTs; Arabidopsis thaliana; epigenetic diversity DNA methylation; amplicon sequencing; NUMTs; Arabidopsis thaliana; epigenetic diversity
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Yoshida, T.; Tarutani, Y.; Kakutani, T.; Kawabe, A. DNA Methylation Diversification at the Integrated Organellar DNA-Like Sequence. Genes 2018, 9, 602.

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