title: Differential methylation of genes and repeats in land plants.
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.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland 20850, USA.
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
authors.forename: Robert
authors.initials: R
authors.lastname: Citek
authors.forename: Muhammad A
authors.initials: MA
authors.lastname: Budiman
authors.forename: Andrew
authors.initials: A
authors.lastname: Nunberg
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Bedell
authors.forename: Nathan
authors.initials: N
authors.lastname: Lakey
authors.forename: Andrew L
authors.initials: AL
authors.lastname: O'Shaughnessy
authors.forename: Lidia U
authors.initials: LU
authors.lastname: Nascimento
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Robert A
authors.initials: RA
authors.lastname: Martienssen
mesh_terms: D019175:DNA Methylation; D020440:Gene Duplication; D017343:Genes, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid