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.

Figure 1.

Phylogenetic tree showing approximate evolutionary distances among the plant species used in this study. The corresponding gene enrichment factor (GEF) is shown in parenthesis.

Figure 2.

Percentage of genes in each WGS set of sequences. (A) Monocots. The expected number is calculated relative to rice (see Methods). (B) Dicots. The expected number is calculated relative to Arabidopsis (C) Non-angiosperms. The expected number is calculated relative to rice.

Figure 3.

Gene enrichment for each species. (A) Monocots. The expected GEF is calculated by extrapolation of the gene frequency found in rice to a genome of the corresponding size. (B) Dicots. The expected GEF is calculated by extrapolation of the gene frequency found in soybean to a genome of the corresponding size. (C) Same as B using tomato as a reference. (D) Non-angiosperms. The expected GEF is calculated by extrapolation of the gene frequency found in rice to a genome of the corresponding size. The GEF values are listed in Supplemental Table 1, and a list of all gene matches is shown in Supplemental Table 2.

Figure 4.

Frequency of McrBC recognition sites in genes and repeats in each WGS or MF set of sequences. (A) Monocots, (B) dicots, (C) non-angiosperms. A classification of repeat content in each genome is described in Supplemental Table 3.