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, Joshua A. Udall, Chiedozie Egesi, Jeremy Schmutz, Jane Grimwood, Scott A. Jackson, Nathan M. Springer, Robert J. Schmitz

Research output: Contribution to journalArticlepeer-review

178 Scopus citations

Abstract

Background: DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. Results: 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. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. Conclusions: These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Original languageEnglish (US)
Article number194
JournalGenome biology
Volume17
Issue number1
DOIs
StatePublished - Sep 27 2016

Bibliographical note

Funding Information:
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 to JS. We thank the Joint Genome Institute and collaborators for access to unpublished genomes of B. rapa, S. viridis, P. virgatum, and P. hallii. This work was supported by the National Science Foundation (NSF) (MCB -1339194), by the Office of the Vice President of Research at UGA, and by The Pew Charitable Trusts to RJS. CEN was supported by a NSF postdoctoral fellowship (IOS - 1402183). We would like to thank Drs. J. Chris Pires, Scott T. Woody, Richard M. Amasino, Heinz Himmelbauer, Fred G. Gmitter, Timothy R. Hughes, Rebecca Grumet, CJ Tsai, Karen S. Schumaker, Kevin M. Folta, Marc Libault, Steve van Nocker, Steve D. Rounsely, Andrea L. Sweigart, Gerald A. Tuskan, Thomas E. Juenger, Douglas G. Bielenberg, Brian Dilkes, Thomas P. Brutnell, Todd C. Mockler, Mark J. Guiltinan, and Mallikarjuna K. Aradhya for providing tissue and DNA of various species used in this study. We would also like to thank the Georgia Genomics Facility and Georgia Advanced Computing Resource Center (GACRC) for technical support, particularly Dr. Shanho Tsai and Yecheng Huang of the GACRC for their efforts.

Publisher Copyright:
© 2016 The Author(s).

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