Enrich for Chloroplast DNA

Chloroplasts are found in all green plants. Its DNA harbors valuable traits and its conservation helps to identify (sub)species in complex plant mixtures.

ChloroplastScan is a tool for in-depth research on the chloroplast and mitrochondrial DNA.

ChloroplastScan benefits:

– No fractionation of the plants necessary due to total DNA as starting material
– Unbiased method that shows the genetic variation of all chloroplasts present
– No PCR steps required to enlarge the fraction of cpDNA before sequencing
– Interrogates all unmethylated DNA, with the majority of the sequences being cpDNA
– Can be used to identfy species in complex mixtures
– Cost-efficient alternative for chloroplast and mitochondria isolation kits0

ChloroplastScan is developed to enrich for chloroplast (cpDNA) and mitochondrial DNA (mtDNA) from DNA samples derived from the whole plant. Current methods involve ultra-centrifugation or extensive lysis-precipitation cycles. Overall, these older methods require large amounts of DNA and are very labor-intensive.

With ChloroplastScan, isolation of organelles is no longer necessary. The total DNA sample is incubated with an antibody against methylated nucleotides. This fraction is then removed, leaving the unmethylated DNA regions intact. The remaining mitochondrial, chloroplast and microbial DNA can then be analyzed by Next Generation Sequencing.

Enrichment method of Chloroplast and Mitochondrial DNA

The size of Chloroplast DNA ranges from 120 to 160 kb, which is relatively small compared to the total genome of plants (Size range 81 Mb (U. gibba) to 150 Gb (P. japonica). For cost-efficient analyses, an enrichment step preceding the sequencing of the organism is compulsory.

The bigger the genome of the plant, the more important is the efficient removal of genomic DNA. In our validation study we assessed the cpDNA enrichment of multiple samples originating from two different species: radish and onion (genomes of respectively 151 Mb and 18 Gb). Depending on the species, 40.5% to 74.6% of the reads could be mapped to the cpDNA and mtDNA reference. Especially for the extremely large genome of the onion, the level of cpDNA enrichment reaches up to 40.000 fold.

We provide detailed analysis for:

Plant samples
– Identification of specific features on the chloroplast and mitochondrial DNA
– Identification of plants in complex ecosystems
– Protection of intellectual property rights
– BioSecurity and management of wild plant populations of rare / endangered plants

Soil and water samples
– Identification of plants in ecological studies

Food products
– Identification of plant components in whole and processed foods.
– Quality and safety control: ensure authenticity of labelling and to ensure food safety.

Pharmaceutical products
– Microbial contamination detection in pharmaceutical products, quality control during drug manufacturing, etc.


Complex ecological questions can be answered with ChloroplastScan. We identify plants in complex ecological mixtures. This analysis method also retains bacterial DNA attached to the plants and is therefore suitable to measure intricate plant-bacteria interactions.

Chloroplast DNA measurement is widely used in many fields of biology such as phylogenetics, evolutionary biology, plant barcoding and identification


A GenomeScan brand

ServiceXS is our research department for genetic analyses. Our scientists constantly test and develop technologies and applications to stay one step ahead in genetic testing. We offer a wide range of applications for veterinary, agriculture, microbial and medical research.