On site DNA barcoding by nanopore sequencing

Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full explo...

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Bibliographic Details
Published in:PloS one Vol. 12; no. 10; p. e0184741
Main Authors: Menegon, Michele, Cantaloni, Chiara, Rodriguez-Prieto, Ana, Centomo, Cesare, Abdelfattah, Ahmed, Rossato, Marzia, Bernardi, Massimo, Xumerle, Luciano, Loader, Simon, Delledonne, Massimo
Format: Journal Article
Language:English
Published: United States Public Library of Science 04.10.2017
Public Library of Science (PLoS)
Subjects:
Amphibia
Amphibians
Amphibians - classification
Amphibians - genetics
Animals
Base Sequence
Biodiversity
Bioinformatics
Biology and life sciences
Biotechnology
Computer and information sciences
Cytochrome
Data analysis
Data processing
Deoxyribonucleic acid
Digitization
DNA
DNA Barcoding, Taxonomic
DNA sequencing
Ebola virus
Ebolavirus
Ecology and Environmental Sciences
Endangered & extinct species
Environmental conditions
Exploitation
Extinction
Forests
Gene sequencing
Genetic markers
Genomes
Genomics
High-Throughput Nucleotide Sequencing - methods
Identification
Laboratories
Laboratory equipment
Mimicry
Museums
Nanopores
Nucleotide sequence
Organisms
Porosity
Portable equipment
Rainforests
Reagents
Reptiles
Reptiles - classification
Reptiles - genetics
Research and Analysis Methods
Sequence Homology, Nucleic Acid
Species
Surveillance
Taxonomy
Tropical Climate
Tropical environment
Tropical environments
Vertebrates
Italy
ISSN:1932-6203, 1932-6203
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Summary:Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.
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Competing Interests: The authors and Personal Genomics reported no conflict of interests for the work described here. Affiliation to Personal Genomics does not alter our adherence to PLOS ONE policies on sharing data and materials.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0184741