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GoEnrich: creating high quality genomic DNA resources from limited voucher specimen tissues or museum specimens of at-risk species for conservation-friendly use in the validation of environmental DNA assays.

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  • معلومة اضافية
    • المصدر:
      Publisher: Biomed Central Country of Publication: England NLM ID: 101462768 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-0500 (Electronic) Linking ISSN: 17560500 NLM ISO Abbreviation: BMC Res Notes Subsets: MEDLINE
    • بيانات النشر:
      Original Publication: London : Biomed Central, 2008.
    • الموضوع:
      Museums* ; DNA, Environmental*/genetics ; DNA, Environmental*/analysis; Animals ; Conservation of Natural Resources/methods ; Endangered Species ; Nucleic Acid Amplification Techniques/methods ; Birds/genetics ; Fishes/genetics ; Genome, Mitochondrial/genetics ; Real-Time Polymerase Chain Reaction/methods
    • نبذة مختصرة :
      Objective: Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed.
      Results: Using fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory C q values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts.
      (© 2024. The Author(s).)
    • References:
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    • Grant Information:
      Postdoctoral fellowship Liber Ero Foundation; 312ITD Genome Canada; 312ITD Genome British Columbia; 312ITD Genome Quebec
    • Contributed Indexing:
      Keywords: At-risk species; Museomics; Whole genome amplification; eDNA assay validation; qPCR
    • الرقم المعرف:
      0 (DNA, Environmental)
    • الموضوع:
      Date Created: 20240910 Date Completed: 20240911 Latest Revision: 20240914
    • الموضوع:
      20240914
    • الرقم المعرف:
      PMC11386110
    • الرقم المعرف:
      10.1186/s13104-024-06936-z
    • الرقم المعرف:
      39256849