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

• DOI: 10.3732/apps.1400064
• Publication Date: 2014-10-30T11:34:32Z
• Authors: Erbay Yigit; David I. Hernandez; Joshua T. Trujillo; Eileen Dimalanta; C. Donovan Bailey
• Keywords: genome sequencing; 0301 basic medicine; enrichment; 03 medical and health sciences; QH301-705.5; QK1-989; Botany; microbiome; Biology (General); endophyte; methyl-binding domain; metagenome

• 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.