Differential methylation of genes and repeats in land plants

  1. Pablo D. Rabinowicz1,2,
  2. Robert Citek3,
  3. Muhammad A. Budiman3,
  4. Andrew Nunberg3,
  5. Joseph A. Bedell3,
  6. Nathan Lakey3,
  7. Andrew L. O'Shaughnessy2,
  8. Lidia U. Nascimento2,
  9. W. Richard McCombie2, and
  10. Robert A. Martienssen2,4
  1. 1 The Institute for Genomic Research, Rockville, Maryland 20850, USA
  2. 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
  3. 3 Orion Genomics, LLC, Saint Louis, Missouri 63108, USA

Abstract

The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration (MF). Therefore, MF has been used as a gene enrichment technology in sorghum and maize, where gene enrichment was proportional to genome size. Here we apply MF to a broad variety of plant species spanning a wide range of genome sizes. Differential methylation of genic and non-genic sequences was observed in all species tested, from non-vascular to vascular plants, but in some cases, such as wheat and pine, a lower than expected level of enrichment was observed. Remarkably, hexaploid wheat and pine show a dramatically large number of gene-like sequences relative to other plants. In hexaploid wheat, this apparent excess of genes may reflect an abundance of methylated pseudogenes, which may thus be more prevalent in recent polyploids.

Footnotes

  • [Supplemental material is available on line at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. CZ897387-CZ899108 and CZ904997-CZ905001 for rice; CZ885111-CZ886935 and CZ904956-CZ904957 for barley; CZ888291-CZ891417 and CZ904958-CZ904975 for bread wheat; CZ899109-CZ902001 and CZ905002-CZ905005 for soybean; CZ886936-CZ888290 for oilseed rape; CZ896505-CZ897386 for potato; CZ902002-CZ904955 and CZ905006-CZ905009 for tomato; CZ891418-CZ892414 and CZ904976-CZ904980 for cotton; CZ893553-CZ894712 for moss; CZ892415-CZ893552 and CZ904981-CZ904996 for fern; and CZ894713-CZ896504 for pine. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: USDA National Plant Germplasm System, A. Kleinhofs, F. Mehdizadegan, B. Gill, J. Mullet, B. Burr, A. Schwartz, and R. Quatrano.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.4100405.

  • ↵4 Corresponding author. E-mail martiens{at}cshl.edu; fax (516) 367-8369.

    • Accepted August 1, 2005.
    • Received April 26, 2005.
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  1. doi: 10.1101/gr.4100405 Genome Res. 15: 1431-1440 Cold Spring Harbor Laboratory Press

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