Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

Wilson, Andrew W.; Eberhardt, Ursula; Nguyen, Nhu; Noffsinger, Chance R.; Swenie, Rachel A.; Loucks, Justin L.; Perry, Brian A.; Herrera, Mariana; Osmundson, Todd W.; DeLong-Duhon, Sarah; Beker, Henry J.; Mueller, Gregory M.

doi:10.3390/jof9080788

Cited by 8 publications

References 72 publications

(105 reference statements)

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Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality

Chua,

Ord,

Bent

et al. 2024

Environmental DNA

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The success of amplicon sequencing studies of environmental DNA (eDNA) depends on the choice of primer pairs used to select taxa‐specific regions of DNA for amplification then sequencing to characterize sample composition. This paper presents practical methods to visualize the extent to which different primer pairs can differentiate taxonomic groups, enabling researchers to assess which primers might be best suited for a study or environment of interest. These methods can also be used to review taxonomic annotations in genomic reference sequence databases. We apply the concept of DNA barcoding gaps to metabarcoding of multiple species in environmental DNA to leverage reference data on the amplicon sequences of previously characterized specimens. Since reference data sets are large and complex, we provide a simple and intuitive method to navigate subsets of reference sequence data containing conflicting or ambiguous relationships between genomic information and taxonomic classification. We demonstrate how to use gap visualization and taxonomic segmentation in comparing how well different primer pairs discriminate species of interest, and in detecting anomalies in reference sequence annotation. We show how these visualization methods can enable amplicon survey study design and make fundamental molecular resources more accessible to a wider research audience beyond bioinformaticians and data scientists.

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Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality

Chua,

Ord,

Bent

et al. 2024

Environmental DNA

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Integrating DNA Barcoding Within an Orthogonal Approach for Herbal Product Authentication: A Narrative Review

Nazar,

Saxena,

Sebastian

et al. 2024

Phytochemical Analysis

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IntroductionExisting methods for morphological, organoleptic, and chemical authentication may not adequately ensure the accurate identification of plant species or guarantee safety. Herbal raw material authentication remains a major challenge in herbal medicine. Over the past decade, DNA barcoding, combined with an orthogonal approach integrating various testing methods for quality assurance, has emerged as a new trend in plant authentication.ObjectiveThe review evaluates DNA barcoding and common alternative testing in plant‐related sectors to enhance quality assurance and accurate authentication.MethodStudies were selected based on their relevance to the identification, quality assurance, and safety of herbal products. Inclusion criteria were peer‐reviewed articles, systematic reviews, and relevant case studies from the last two decades focused on DNA barcoding, identification methods, and their applications. Exclusion criteria involved studies lacking empirical data, those not peer‐reviewed, or those unrelated to the main focus. This ensured the inclusion of high‐quality, pertinent sources while excluding less relevant studies.ResultsAn orthogonal approach refers to the use of multiple, independent methods that provide complementary information for more accurate plant identification and quality assurance. This reduces false positives or negatives by confirming results through different techniques, combining DNA barcoding with morphological analysis or chemical profiling. It enhances confidence in results, particularly in cases of potential adulteration or misidentification of plant materials.ConclusionThis study highlights the persistent challenges in assuring the quality, purity, and safety of plant materials. Additionally, it stresses the importance of incorporating DNA‐based authentication alongside traditional methods, to enhance plant material identification.

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How to best detect threatened deadwood fungi – Comparing metabarcoding and fruit body surveys

Rieker,

Runnel,

Baldrian

et al. 2024

Biological Conservation

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Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

Cited by 8 publications

References 72 publications

Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality

Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality

Integrating DNA Barcoding Within an Orthogonal Approach for Herbal Product Authentication: A Narrative Review

How to best detect threatened deadwood fungi – Comparing metabarcoding and fruit body surveys

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