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Widespread natural variation of DNA methylation within angiosperms

Chad E. Niederhuth, Adam J. Bewick, Lexiang Ji, Magdy S. Alabady, Kyung Do Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, John M. Burke, Josh A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer, Robert J. Schmitz
doi: https://doi.org/10.1101/045880
Chad E. Niederhuth
1Department of Genetics, University of Georgia, Athens, GA 30602, USA,
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Adam J. Bewick
1Department of Genetics, University of Georgia, Athens, GA 30602, USA,
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Lexiang Ji
2Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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Magdy S. Alabady
3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Kyung Do Kim
4Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
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Qing Li
5Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
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Nicholas A. Rohr
1Department of Genetics, University of Georgia, Athens, GA 30602, USA,
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Aditi Rambani
6Plant and Wildlife Science Department, Brigham Young University, Provo, Utah 84602, USA
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John M. Burke
3Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Josh A. Udall
5Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN 55108, USA
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Chiedozie Egesi
7National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia 440001, Nigeria
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Jeremy Schmutz
8HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
9Department of Energy Joint Genome Institute, Walnut Creek, California, USA
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Jane Grimwood
8HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
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Scott A. Jackson
4Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
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Nathan M. Springer
6Plant and Wildlife Science Department, Brigham Young University, Provo, Utah 84602, USA
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Robert J. Schmitz
1Department of Genetics, University of Georgia, Athens, GA 30602, USA,
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Abstract

To understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time. These results show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

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Posted May 30, 2016.
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Widespread natural variation of DNA methylation within angiosperms
Chad E. Niederhuth, Adam J. Bewick, Lexiang Ji, Magdy S. Alabady, Kyung Do Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, John M. Burke, Josh A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer, Robert J. Schmitz
bioRxiv 045880; doi: https://doi.org/10.1101/045880
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Widespread natural variation of DNA methylation within angiosperms
Chad E. Niederhuth, Adam J. Bewick, Lexiang Ji, Magdy S. Alabady, Kyung Do Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, John M. Burke, Josh A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer, Robert J. Schmitz
bioRxiv 045880; doi: https://doi.org/10.1101/045880

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