Breaking down DNA by genome

October 31, 2014, American Journal of Botany

New DNA sequencing technologies have greatly advanced genomic and metagenomic studies in plant biology. Scientists can readily obtain extensive genetic information for any plant species of interest, at a relatively low cost, rapidly accelerating the pace of genome sequencing.

However, since harbor three separate genomes (nuclear, chloroplast, and mitochondrial), it can often be challenging to isolate the particular genome of interest from extracted DNA samples. Sequencing DNA containing all three genomes therefore results in a considerable amount of wasted data, for example, if only the chloroplast genome is desired for the study.

Methods exist to isolate particular genomic regions, but each of these has drawbacks. For example, some protocols require extensive lab work, while others (e.g., long-range PCR and hybrid enrichment) require prior knowledge of the genomic regions of interest.

A new method by researchers from New England Biolabs and New Mexico State University provides plant biologists with a quick and simple approach for separating plant nuclear DNA from organellar DNA for genomic and metagenomic studies. The approach, published in the November issue of Applications in Plant Sciences, targets the methyl-CpG-binding domain, following a similar method applied for genomic studies of humans.

The method relies on differences in CpG methylation between nuclear and organellar (i.e., chloroplast and mitochondrial) genomes in plants. Compared to the nuclear genome, the chloroplast and mitochondrial genomes essentially lack CpG methylation (i.e., the addition of methyl groups to sites in the genome where cytosine and guanine occur side by side).

Given these different methylation patterns, the researchers used specialized magnetic beads that hybridize with methyl-CpG-rich DNA regions in an attempt to separate nuclear DNA from organellar DNA in total genomic DNA samples. They then sequenced the methyl-enriched portion and the methyl-depleted portion separately. They found that the methyl-enriched sample contained a considerable increase in concentration of nuclear DNA, while the methyl-depleted sample contained an increased concentration of organellar DNA.

Dr. Donovan Bailey, senior author of the study and professor at New Mexico State University, said this approach has several advantages over previously established methods for enriching either nuclear or organellar DNA for .

"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 studied, other than the domain of origin—nuclear, organellar, or prokaryote. Furthermore, not requiring extensive starting material and the speed are benefits relative to some methods."

According to Bailey, this approach can also be used to target genomes of endophytes (i.e., fungi that live in plants) and prokaryotic parasites in plant DNA samples. Endophyte genomes undergo CpG methylation, while prokaryotic genomes do not, making it easy to sequence either of these along with the particular plant (s) of interest. This will provide researchers with greater insight on the diversity of other eukaryotes and prokaryotes living inside plant tissues.

Although this study focused on flowering , Bailey said the approach will likely work well across other major plant groups (e.g., ferns, gymnosperms).

Explore further: Sequencing hundreds of chloroplast genomes now possible

More information: Erbay Yigit, David I. Hernandez, Joshua T. Trujillo, Eileen Dimalanta, and C. Donovan Bailey. Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues. Applications in Plant Sciences 2(11): 1400064. DOI: 10.3732/apps.1400064

Related Stories

Sequencing hundreds of chloroplast genomes now possible

January 31, 2013

Researchers at the University of Florida and Oberlin College have developed a sequencing method that will allow potentially hundreds of plant chloroplast genomes to be sequenced at once, facilitating studies of molecular ...

Getting a jump on plant-fungal interactions

July 29, 2014

Fungal plant pathogens may need more flexible genomes in order to fully benefit from associating with their hosts. Transposable elements are commonly found with genes involved in symbioses.

Recommended for you

Japan to make crater on asteroid to get underground samples

March 18, 2019

Japan's space agency said Monday that its Hayabusa2 spacecraft will follow up last month's touchdown on a distant asteroid with another risky mission—dropping an explosive on the asteroid to make a crater and then collect ...

Bright X-ray galactic nuclei

March 18, 2019

All massive galaxies are believed to host supermassive black holes (SMBH) at their centers that grow by accreting mass from their environment. The current picture also imagines that the black holes grow in size as their host ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.