MinION-based DNA barcoding of preserved and non-invasively collected wildlife samples
| Autor: | Marisa C. W. Lim, Tracie A. Seimon, Denise McAloose, Adeline Seah, Stefan Prost |
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| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine field-friendly lcsh:QH426-470 Sample (material) Preservation Biological Biomeme MinION Animals Wild Computational biology Biology FFPE 010603 evolutionary biology 01 natural sciences DNA barcoding Article 03 medical and health sciences Genetics Consensus sequence Animals DNA Barcoding Taxonomic Panthera Genetics (clinical) Wildlife conservation Computational Biology High-Throughput Nucleotide Sequencing Biodiversity DNA extraction lcsh:Genetics DNA sequencer 030104 developmental biology Ducks Minion Nanopore sequencing Chelex non-invasive sampling |
| Zdroj: | Genes Volume 11 Issue 4 Genes, Vol 11, Iss 445, p 445 (2020) |
| Popis: | The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%&ndash 100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification. |
| Databáze: | OpenAIRE |
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