Crop diseases caused by fungal, bacterial, and viral pathogens can lead to devastating yield losses and threaten global food security. Early detection and accurate tracking are key to preventing outbreaks and managing resistance. Amplicon sequencing offers a powerful solution by providing high-resolution insights into the genetic makeup of pathogens, helping researchers and growers monitor disease dynamics.
At Paragon Genomics, our targeted NGS technologies enable scientists to identify multiple pathogens simultaneously, detect resistance genes, and follow their spread across growing seasons and regions; all within a single, streamlined workflow.
What Problems Do Researchers Face in Crop Pathogen Surveillance?
Monitoring plant pathogens presents several persistent challenges, including:
- Mixed infections often occur, making it difficult to identify all species with traditional culture or PCR methods.
- Low-abundance pathogens can go undetected until they cause visible damage.
- Resistance genes evolve quickly, requiring ongoing surveillance of pathogen populations.
- Environmental samples are complex, containing host DNA, soil microbes, and contaminants that can interfere with detection.
- Outbreaks demand rapid results, but conventional workflows can be slow and labor-intensive.
These challenges have driven the need for sequencing-based surveillance tools that combine sensitivity, scalability, and precision—qualities that amplicon sequencing delivers with ease.
How Does Amplicon Sequencing Improve Pathogen Detection?
Amplicon sequencing enhances pathogen surveillance by combining high sensitivity with broad detection capabilities. Rather than simply targeting a single organism or gene, researchers can screen for multiple fungal, bacterial, and viral species in one sequencing run. This approach captures both known and emerging pathogens (even at a very low abundance), offering a clearer picture of disease pressure within crops.
By focusing on specific genomic regions linked to virulence or resistance, amplicon sequencing also reveals genetic variants that influence how pathogens respond to control measures. These insights help researchers track resistance development, identify new outbreak strains, and support data-driven disease management strategies across agricultural systems.
How Does Targeted Sequencing Work in Pathogen Monitoring?
Targeted sequencing workflows begin with the selection of genomic regions that distinguish pathogens from host DNA or other microbes. For example, researchers might target the internal transcribed spacer (ITS) region for fungi, the 16S rRNA gene for bacteria, or coat protein genes for viruses. Using a multiplexed amplicon approach, these regions are amplified, then sequenced, and analyzed to identify each pathogen and its genetic variants.
Paragon Genomics’ CleanPlex and AgriType® solutions simplify this process with customizable panels and an efficient, single-tube workflow. The resulting data provide high-resolution profiles that reveal which pathogens are present, how abundant they are, and whether resistance genes are emerging. All of which is important information for guiding breeding, use of pesticides, and long-term pathogen management.
Why Use Paragon Genomics’ Amplicon NGS Solutions for Pathogen Surveillance
Paragon Genomics’ amplicon NGS technology combines precision, flexibility, and efficiency to support every stage of pathogen monitoring. Our customizable panels allow researchers to design assays that target specific pathogens or resistance genes of interest—whether the goal is to monitor fungal, bacterial, or viral populations.
The CleanPlex chemistry delivers high-quality libraries with a streamlined, single-tube workflow optimized for agricultural samples. This approach reduces handling time, minimizes contamination risk, and produces consistent, reproducible results across studies. AgriType® solutions can be scaled for regional, national, or global surveillance programs, enabling comprehensive tracking of emerging disease threats.
By offering fast turnaround, broad detection capabilities, and compatibility with leading sequencing platforms, Paragon Genomics helps agricultural researchers and biosecurity teams stay ahead of evolving pathogens, therefore protecting yields and strengthening long-term crop resilience.
Amplicon Sequencing with Paragon Genomics
Amplicon sequencing is transforming agricultural pathogen surveillance by giving researchers the power to detect, identify, and track fungal, bacterial, and viral threats with precision. At Paragon Genomics, we are advancing plant health and disease management through targeted NGS solutions that help scientists monitor resistance genes, study pathogen evolution, and safeguard global crop productivity.
Our commitment to innovation ensures that researchers have the tools they need to strengthen pathogen monitoring programs and drive progress in sustainable agriculture.
Paragon Genomics
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