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Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries.

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  • معلومة اضافية
    • المصدر:
      Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
    • بيانات النشر:
      Original Publication: San Francisco, CA : Public Library of Science
    • الموضوع:
      Nanopore Sequencing*/methods ; DNA, Environmental*/genetics ; DNA, Environmental*/analysis ; DNA Barcoding, Taxonomic*/methods; Zambia ; Biodiversity ; Animals ; Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing
    • نبذة مختصرة :
      Competing Interests: Enter: The authors have declared that no competing interests exist.
      Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers a cost- and time-efficient alternative to conventional biodiversity surveys, enabling detection of rare, cryptic, and elusive species from environmental samples. However, limited access to genomic technologies restricts the application of eDNA metabarcoding in highly biodiverse remote regions and low- and middle-income countries (LMICs). Here, we directly compared the latest portable nanopore sequencing methods with established Illumina sequencing for vertebrate eDNA metabarcoding of Zambian water samples. Our results show that due to recent improvements in sequencing chemistry and optimized basecalling, nanopore sequencing data can recapitulate or even surpass established protocols, demonstrating the feasibility of in situ biodiversity assessments. eDNA- and camera trap-based species detections had minimal overlap in species detections, suggesting a complementary rather than substituting application of these biodiversity monitoring technologies. We finally demonstrate that our entire eDNA workflow can be successfully implemented in a mobile laboratory under remote field conditions by completing all steps-from sample collection to data analysis-within the Luambe National Park in Zambia. This approach has important implications for capacity building in LMICs and for overcoming limitations associated with sample export.
      (Copyright: © 2025 Gygax et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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    • الرقم المعرف:
      0 (DNA, Environmental)
    • الموضوع:
      Date Created: 20251016 Date Completed: 20251016 Latest Revision: 20251019
    • الموضوع:
      20251019
    • الرقم المعرف:
      PMC12530551
    • الرقم المعرف:
      10.1371/journal.pone.0333994
    • الرقم المعرف:
      41100571