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MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples
Open AccessArticle

Takeaways from Mobile DNA Barcoding with BentoLab and MinION

1
Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
2
Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
*
Authors to whom correspondence should be addressed.
These authors contributed equally.
Genes 2020, 11(10), 1121; https://doi.org/10.3390/genes11101121
Received: 22 August 2020 / Revised: 17 September 2020 / Accepted: 22 September 2020 / Published: 24 September 2020
(This article belongs to the Special Issue MetaGenomics Sequencing In Situ)
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters’ Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended. View Full-Text
Keywords: cytochrome c oxidase subunit I (COI); marine biodiversity; metazoa; next-generation sequencing (NGS); Oxford Nanopore Technologies (ONT); portable sequencing cytochrome c oxidase subunit I (COI); marine biodiversity; metazoa; next-generation sequencing (NGS); Oxford Nanopore Technologies (ONT); portable sequencing
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Chang, J.J.M.; Ip, Y.C.A.; Ng, C.S.L.; Huang, D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes 2020, 11, 1121.

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