Genome and metagenome sequencing: Using the human methyl‐binding domain to partition genomic DNA derived from plant tissues

Abstract

• Premise of the study: Variation in the distribution of methylated CpG (methyl-CpG) in genomic DNA (gDNA) 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.• Methods: MBD2 has been used to enrich prokaryotic DNA in animal systems. Using gDNA 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.• Results: Relative to untreated gDNA, the methyl-depleted libraries showed a 3.2–11.2-fold and 3.4–11.3-fold increase in chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA), respectively. Methyl-enriched fractions showed a 1.8–31.3-fold and 1.3–29.0-fold decrease in cpDNA and mtDNA, respectively.• Discussion: 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.

Phylogenomics and barcoding of Panax: toward the identification of ginseng species

“…The novel method based on methylation-based enrichment increased the concentration of plastid DNA by 30% which is in the range found by a previous pilot study [ 84 ]. It is a suitable method for enriching the organellar genome before sequencing.…”

“…enriched for plastid) and a methylation-rich fraction (e.g. depleted in plastid) [ 84 ]. This method has the advantage that it uses a small quantity of dry material (below 40 mg) and is suitable for non-model organisms.…”

Strategies for complete plastid genome sequencing

“…Yigit et al . () showed that gDNA could be partitioned into a high‐methylated‐CpG nuclear fraction, and a fraction of low‐methylated‐CpG elements. The methyl‐poor fraction was enriched for plastids by 3.2‐ to 11.2‐fold, depending on the species in question.…”

Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost

“…For example, Feehery et al ( 111 ) used magnetic beads with methyl-binding domains that specifically bind to a portion of mammalian and fish DNA to reduce the presence of these nontarget molecules (also see reference 112 ) (commercially available kits include the NEBNext microbiome DNA enrichment kit). Yigit et al ( 113 ) extended this approach to plant tissues and selectively shifted the ratio of nuclear to organellar DNA obtained from five model angiosperm taxa (also see reference 114 ).…”