Identification of Pests by DNA Barcoding and DNA Metabarcoding

The importance of DNA barcoding for the official diagnosis of regulated pests was recognised by the International Standards of Phytosanitary Measures (ISPM nº 27) back in 2006. At AllGenetics we provide you with an accurate pest identification service which is based on the DNA barcoding and DNA metabarcoding methods. With our service you will be able to identify your pest to the species level in a reliable and cost-effective way.

What bug is eating my crops?

Identifying pests to the species level has traditionally been based on morphological analysis. However, the more non-indigenous species there are, the fewer trained taxonomists for each organismal group are to be found in control agencies. Therefore, DNA barcoding has become the method of choice for a rapid, reliable, and cost-effective identification of pest species.

As soon as eggs are laid...

In the particular case of invertebrate pests, DNA barcoding can not only correctly diagnose adult specimens but identify eggs and larvae to the species level as well. This makes it a very powerful method, as proper phytosanitary measures can be applied even before the eggs hatch, so to a great extent crop damage can be prevented.

...and before seeds are sowed

Seed-borne pathogens represent a major threat to crop yield and quality. Since infested seeds can be asymptomatic, pathogens can easily remain undetected after visual inspection of a seed lot. Thus, DNA-based methods represent a valuable alternative for the early detection of seed-transmitted pests, reducing the risk of pathogen introduction in susceptible crops.

Our expertise in DNA barcoding covers most plant pests and pathogens, including insects, mites, nematodes, fungi, and bacteria (click here for a complete list of species). If your target species is not in the list, please, do not hesitate to contact us and let us know about your specific testing requirements.

NGS technologies to identify unsuspected pest species

Thanks to our experience with next-generation sequencing, we can carry out custom-tailored projects to simultaneously detect multiple pathogen species in a single analysis. Among its multiple applications, this approach is particularly useful for the culture-free profiling of microbial diversity either in plant material or environmental samples (soil, air, water).

More importantly, as it requires no previous knowledge of the species composition in a sample, this NGS-based service may enable the identification of new, unsuspected pest species and, therefore, the development of effective disease management strategies.

A quality assurance tool for biological control programs

Biological control programs – the use of natural enemies to suppress and maintain populations of a target pest species – are becoming more and more important in crop protection. Since most natural enemies are highly specialised, correctly identifying these species is a cornerstone for any successful biological control strategy.

Through our DNA-based service, we provide commercial growers and suppliers with an added quality assurance that certifies the identity of the species sold for biological control programs and bioefficacy assays.

How we work

We provide sampling kits and sample collection guidelines within 2-4 working days once your order has been placed.

DNA barcoding projects involve DNA isolation, PCR amplification of a genome region (the DNA barcode) from the sample, and sequencing. Subsequently, electropherograms are analysed and the sequences obtained are compared to those in reference databases to find the matching species.

In DNA metabarcoding projects, we construct amplicon libraries, which are then sequenced in the appropriate next-generation sequencing platform. The millions of next-generation sequencing reads obtained are processed using a specific bioinformatic pipeline, to cluster the reads into taxonomic units.

Deliverables include a species identification certificate, the raw data generated (which will be delivered through our server), and a summary of the methods followed. For both DNA barcoding and metabarcoding projects, we provide a free archiving service for your own sequences. These sequences will be used as an additional reference database in your future orders.