The Illusion of DNA as the Oracle of Delphi
One of the primary reasons for the failure of DNA testing companies in the natural products industry to date is the misconception that DNA is some sort of all-knowing and infallible source of information. This "Oracle of Delphi" mentality spreads the misconception that DNA can answer any question about a product's identity and composition all at once. In reality, DNA analysis is a powerful tool, but like any approach or method has limitations. You need to be working with experts in both genetics and botany to not only use the right markers but understand the results.
Not All DNA Markers Are Equal
Several of the companies that have failed over the years relied on popular barcoding genes and universal markers for product identification. These tools are valuable for academic or evolutionary studies, but they’re not always suitable for species delineation in commercial products. For example, the internal transcribed spacer (ITS) region is a nonfunctional DNA sequence found between the small and large subunits of ribosomal RNA (rRNA) genes. It’s a highly variable region that is useful for studying the evolutionary relationships between species and genera, and has been frequently adopted for species ID in natural products. However, it is now recognized asproblematic for species identification in many lineages.
Asking the Wrong Question
Another key flaw in the DNA testing approach taken by companies who struggled was asking the generic question, "What is this?", instead of the specific question, "Is this material Species X?". The first question inevitably leads to what I call a "fishing method" approach, where sequences are compared against large databases like the National Center for Biotechnology Information (NCBI). Relying solely on this method is problematic for two reasons:
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Representation: The amount and distribution of data across the tree of life in these databases are highly variable.
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Quality of Data: There is often insufficient Certified Reference Material (CRM) and many database accessions are mislabeled.
These problems are particularly acute for rare and understudied taxa as well as taxa that fall outside of the interest of BigAg, like medicinal plants, which are ironically often the focus of such testing methods. People often assume that common medicinal plants in dietary supplements would be well represented. This is not the case. For example, whereas soybean has 2.45M sequences, maca is represented by only 114. Chaga is represented by 267 sequences. And these are just small fragment sequences, not genomes, to say nothing of whether the sample submitted itself was accurately labeled.
Issues With the Database
Speaking of databases, the reliability of DNA testing is heavily dependent on the quality and comprehensiveness of reference databases, and these databases suffer from two extremes:
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Too Few Sequences: Some species have zero or very limited representative sequences that result in incorrect matches or excessive computing time trying to match them.
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Too Many Sequences: Overrepresented species in the database can lead to frequent false matches and overshadow closely related species.
Taking The Right Approach: Species-Specific Markers
A more targeted approach is necessary to overcome these types of challenges. Instead of relying on universal markers, companies should focus on developing robust sets of species specific markers. It necessitates a comprehensive knowledge of the genes or genetic regions used as markers, and a thorough understanding of the global supply chain for the organism(s) in question. This requires a deep understanding of the organism's population genetics, life history and mating system.
Several complications must be addressed and overcome for successful DNA test development. Ancestral polymorphism and incomplete lineage sorting can lead to conflicts between species trees and gene trees—a phenomenon that can occur at the species AND population levels. Appropriate sampling is also crucial to capture the genetic diversity within and between species. Hybridization and evolving nomenclature further complicate attempts at accurate identification. Chemistry test development has the same issues in these regards.
In summary, prior failures of using DNA in the natural products industry in years past stems from either a lack of training in genetics, a lack of understanding of the biology of the system in which genetics are being applied, a lack of understanding of the global supply chain, or an overreliance on inappropriate phylogenetic markers.
Moving Forward With Robust DNA Test Development
To develop DNA tests for species identification in natural products, companies should consider the following protocols:
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Collect diverse reference material within target species and common adulterants
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Authenticate species identity using a mycologist or botanist.
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Perform deep sequencing to construct pan-genome-type reference tools
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Identify genomic regions that are both inclusive of all target taxa and exclusive to sister species and known adulterants
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Validate assays on a wide set of diverse matrices
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Seek third-party validation of results
By utilizing organizations built for botanical supply chain DNA testing likeLeafWorks, the natural products industry can enjoy the benefits of robust DNNA assays. Shifting focus to species-exclusive markers and adopting a more targeted approach is how DNA should be applied to our industry, and it is how we approach all of our test development.
This approach requires significant upfront investment in sampling, sequencing and analysis, but it ultimately yields a highly cost-effective, rapid and scalable assay for accurate product testing. As the industry moves forward, we must all recognize that DNA is not an all-knowing oracle but rather a powerful tool that when developed correctly can significantly and radically enhance product quality and consumer trust.
Interested in Partnership or Trying Us Out?
Are you a third party lab interested in boosting revenue alongside your chemistry testing to support clients interested in complementary methods? Are you a product maker using functional mushrooms looking for quality control? We want to work with you! TheLeafWorks® Mushroom DNA ID Tests are available for ordering via our website or as third-party sales. Partner with LeafWorks and see how authenticity is in our DNA.
