Location: US, NA

PDQeX phytoGEM

Suitable for studying plant genotypes and genetic variation, endophytic plant pathogens, genetic mapping, fingerprinting, microsatellite marker-assisted selection, and for evaluating the authenticity of exported plant varieties, botanical extracts and molecular detection of food adulterant.

Produces double-stranded DNA suitable for PCR and qPCR.

Each kit contains PDQeX prepGEM, Histosolv, enhancer, GREEN+ buffer, and extractor tubes.

For processing larger samples, we recommend the PDQeX phytoGEM HC kits. These kits have the traditional advantages that come with using the PDQeX Nucleic Acid Extractor but also include the new HC extraction cartridges.

These new HC extraction cartridges allow for more sample to be loaded into the cartridge before the purification matrix becomes overloaded. This results in a higher final yield of extracted DNA, meaning the PDQeX phytoGEM HC kits are better suited for sequencing workflows where a higher yield of DNA is encouraged.

info Product Codes and Prices
# of Reactions Product Code Price
50 XPP0050 $230.00
100 XPP0100 $440.00
500 XPP0500 $2,100.00
1000 XPP1000 $3,970.00
50 HC XPH0050 $230.00
100 HC XPH0100 $440.00
500 HC XPH0500 $2,100.00
1000 HC XPH1000 $3,970.00

Image shows 100, 500, and 1,000 reaction kits, tubes, and phytocards

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The PDQeX phytoGEM kit offers a simple hands-off method for DNA extraction and purification of a variety of plant samples.

Using MicroGEM’s PDQeX Nucleic Acid Extractor, there are only two simple steps – quick sample prep and closed tube automated DNA extraction and purification. The method provides quicker turn-around time for all plant sample types, even your toughest challenges.

  • Thermophilic proteinase and mesophilic cell wall degrading glycosyl hydrolases lyse cells, destroy nucleases, digest protein and release DNA
  • Streamlined approach provides plant to PCR-ready DNA from up to 24 samples of plant tissue, fungi or plant pathogens in less than 15 minutes
  • Easy sampling (such as crushing leaves onto a storage card) provides a long-term storage solution
  • Flexibility to use homogenized leaves or ground plant tissue – whichever sample prep suits your needs
  • Quick sample prep frees up technician time, reduces lab costs, and speeds up response time
  • Disposable, sealed tube protects the integrity of the sample
  • Superior removal of inhibitors
  • Simplified workflow and quick DNA extraction result in faster answers and interventions

PDQeX Handbook (pdf)

phytoGEM Quick Start Card (pdf)
phytoGEM Quick Start Card (HC) (pdf)

phytoGEM Booklet (pdf)

Safety Data Sheet: phytoGEM (pdf)
Safety Data Sheet: phytoGEM (HC) (pdf)

App Note: Using the phytoGEM DNA extraction method with the Hydrocycler (pdf)

App Note: A solution for DNA analysis of plants with minimal sample input using phytoGEM in combination with SolisFAST SolisGreen qPCR mix (pdf)


Extracting DNA from plants can be challenging because of their tough cell walls and the inhibitory polysaccharides and tannins released during the extraction process.  Tissue grinding followed by silica beads, columns or organic solvents becomes a multistep process, both labor-intensive and time-consuming.

The PDQeX phytoGEM kit provides a simple hands-off approach to produce high-quality DNA extraction for most plant-based molecular studies.

Sample prep is easy:

  • a quick punch of the leaf sample onto a storage card
  • also suitable for homogenized or ground plant tissues – whichever sample prep suits your needs
  • no freezing or degradation of the sample.

The PDQeX closed tube system uses our thermophilic proteinase combined with a cocktail of mesophilic cell wall degrading glycosyl hydrolases. These enzymes systematically lyse cells, destroy nucleases, digest proteins, and release DNA. Purification is achieved in the same closed tube system. The entire process, achieved on the PDQeX Nucleic Acid Extractor, achieves PCR-ready DNA in under 15 minutes, helping you to quickly find answers to urgent questions about your plant and your plant’s health.

Application Note: Rapid automated extraction of high-quality plant DNA using phytoGEM and the PDQeX Nucleic Acid Extractor (pdf)

Validated plant species and tissues using the PDQeX phytoGEM approach



Plant Pathogens

Plant diseases cause an estimated 10-20% loss in agricultural productivity worldwide. Many pathogens go untreated resulting in unintended crop destruction due to disease or controlled crop destruction to contain spread. Early detection of pathogens is vital for successful crop management. It allows proactive control measures to be applied well before the establishment and spread of a disease.

Historically, a bottleneck to early detection and pathogen characterization is the DNA extraction process. Current extraction practices are time consuming, often requiring elaborate sample preparation followed by a laborious chemical lysis and purification process.

MicroGEM’s phytoGEM kit provides a simple hands-off approach to DNA extraction ideal for studying endophytic plant pathogens. Using MicroGEM’s proprietary extractor cartridge, precise temperature-controlled enzymatic lysis is performed on the automated PDQeX Nucleic Acid Extractor, helping you quickly find answers to urgent questions about your plant’s health.

phytoGEM has been validated for the detection of the following pathogens:

  1. Bacteria- Xyllela fastidiosa from different fruit trees and berries, Pseudomonassyringae actinidiae (Psa) detection in kiwifruit, Candidatus Liberibacter solanacearum from vector Bactericera cockerelli.
  2. Oomycetes- Phytophthora in kauri, pine and oak.
  3. Phytoplasma in grapevines.
  4. Viruses- Cassava Mosaic Virus, Cassava White Fly Virus.

Shaffer, L. (2019). Inner Workings: Portable DNA sequencer helps farmers stymie devastating viruses. Proceedings of the National Academy of Sciences,116(9), 3351-3353. doi:10.1073/pnas.1901806116. (pdf)
The article describes the ability to screen Cassava crops for Cassava Mosaic Virus (CMV) using MicroGEM's PDQeX for rapid DNA extraction.  The PDQeX was used as the enabling technology to complement DNA sequencing being conducted in the field in real-time.


The introduction of molecular techniques has allowed significant steps to be made in genomics, and in many areas of applied mycology, molecular based approaches have become routine for strain characterization, pathogen detection and identification. Molecular methods are now giving major insights into how fungi function in the environment, where they are present, and how they interact with associated organisms.

DNA extraction from fungi comes with some of the same challenges faced with plants- tough cell walls and inhibitory polyphenols and polysaccharides. Additionally, many fungi are pathogenic and need to be handled carefully.

Conventional DNA extraction methods from fungal cells are very time-consuming or show poor recovery of DNA. PhytoGEM’s enzymatic lysis method effectively extracts DNA from fungal cells using a closed tube system to ensure precise temperature-controlled enzymatic lysis with no harsh chemical washes required. Purification is achieved in the same closed tube system protecting yields while reducing opportunities for contamination.



PDQeX Specifications

Sample capacity
For use with
Voltage (24 V DC adapter included)
Thermal profiles
Programmable thermal range
24 samples, standard 96 well spacing
PDQeX cartridges (200 µL)
5″ touch screen (colour)
100-240 VAC, 2A, 50/60Hz
96 watts at peak draw
Pre-installed & user programmable
22 x 18 x 18.5 cm (L x W x H) (8.5”x 7” x 7.25”)
10.6 Lbs (4.8 kg)


phytoGEM Demonstration

The PDQeX Nucleic Acid Extractor is  the ideal solution for processing tough samples such as plant stems and roots. Thermophilic proteinase and mesophilic cell wall degrading glycosyl hydrolases, used with MicroGEM’s innovative extraction cartridge, provide plant to PCR-ready DNA in less than 15 minutes.  MicroGEM’s phytoGEM approach to plant DNA extraction includes a convenient solution for crushing plant material onto a storage card. It is the ideal solution for extracting high-quality DNA for genotyping, sequencing, and the detection of pathogens.