Genome and Metagenome Sequencing: Using the Human Methyl Binding Domain to Partition Genomic DNA Derived from Plant Tissues (Angiospermae)

Variation in the distribution of methyl-CpG in genomic-DNA across the tree of life is biologically interesting and useful in genomic studies.  We illustrate the use of human methyl-CpG binding domain (MBD2) to fractionate angiosperm DNA into eukaryotic nuclear (methyl-CpG-rich) vs organellar and prokaryotic (methyl-CpG poor) elements for genomic and metagenomic sequencing projects.  MBD2 has been used to enrich prokaryotic DNA in animal systems.   Using genomic DNA from five model angiosperm species, we apply a similar approach to identify whether MBD2 can fractionate plant gDNA into methyl-CpG-depleted vs. enriched methyl-CpG elements.  For each sample three gDNA libraries were sequenced: 1) untreated gDNA; 2) a methyl-CpG-depleted fraction; and 3) a methyl-CpG-enriched fraction.  Relative to untreated gDNA, the methyl-depleted libraries showed a 3.2-11.2- and 3.4-11.3-fold increase in cpDNA and mtDNA, respectively.   Methyl-enriched fractions showed a 1.8-31.3 and 1.3-29.0-fold decrease in cpDNA and mtDNA, respectively.  The application of MBD2 enabled fractionation of plant gDNA.  The effectiveness was particularly striking for monocot gDNA (Poaceae).  When sufficiently effective on a sample, this approach can increase the cost efficiency of sequencing plant genomes as well as prokaryotes living in or on plant tissues.