Separating the plant genome

A new approach to separating plant nuclear DNA from organellar DNA could speed up DNA sequencing and reduce costs. Plant tissues contain three separate genomes – nuclear, chloroplast and mitochondrial – and sequencing DNA containing all three can result in a considerable amount of wasted data if only one is required. A new method developed by researchers at the New Mexico State University and New England Biolabs targets the methyl-CpG-binding domain, relying on differences in CpG methylation between nuclear and organellar – chloroplast and mitochondrial – genomes in plants. CpG methylation – addition of a methyl group – occurs at site in the genome where cytosine and guanine appear side by side, and this is essentially lacking in the organellar genomes. Given these differences, researchers used specialised magnetic beads which hybridise with methyl-CpG-rich DNA regions to separate nuclear DNA from organelle DNA from total DNA samples. They then sequenced the methyl-rich and methyl-depleted portions separately, finding the former contained an considerable increase in concentration of nuclear DNA, while the latter had increase concentrations of organellar DNA. Dr Donovan Bailey, professor at New Mexico State, said this approach offers several advantages over previously established methods. “Our primary perceived benefit includes the development of a means of partitioning DNA by genomic origin when one has no prior knowledge of the genomes being studies, other than the domain of origin – nuclear, oganellar or prokaryote,” he said. “Furthermore, not requiring extensive starting material and the speed are benefits relative to some methods.” Bailey says the approach – which follows a similar method used for genomic studies in humans – could be used to target the genomes of endophytes (fungi that live in plants) and prokaryotic parasites in plant DNA samples. Endophyte genomes undergo CpG methylation, while prokaryote genomes do not, making it easy to sequence either alongside particular plant genomes of interest. This could provide researchers with greater insight on the diversity of other eukaryotes and prokaryotes living inside plant tissues. Genome and Metagenome Sequencing: Using the Human Methyl-Binding Domain to Partition Genomic DNA Derived from Plant Tissues