Time is money: Is the MinION an appropriate alternative for short-read DNA metabarcoding?

Dr Aimee Van Der Reis1, Professor Andrew Jeffs1, Emeritus Professor Lynnath Beckley2

1University Of Auckland, , New Zealand, 2Murdoch University, , Australia

Abstract:

The advent of portable, handheld, sequencing machines such as Oxford Nanopore Technologies MinION devices has led to effective and efficient real-time, on-site sequencing  with a potential turnaround time of 24-48 hours. These devices are generally used for whole genome sequencing and community metagenomics due to their ability to sequence very long DNA strands. However, their on-site practicality is appealing to environmental and dietary DNA researchers as a means of sequencing degraded DNA in a timely manner and thus minimising further loss of DNA quality. A major known limitation of these portable devices is the lower sequencing accuracy (currently 85-95%) compared to that of dedicated short-read platforms (99% accuracy; e.g., Illumina MiSeq). We tested the efficacy of using the MinION Mk1B for analysing the dietary composition of deep-sea lanternfish (ca. 2 cm) sampled from the mesopelagic waters of the of Indian Ocean and compared it to that of the Illumina MiSeq. Two gene regions were targeted, COI and 18S rRNA, with suitable primer sets that produced short reads. The reads were run against curated reference databases and frequent taxa uncovered from dietary content included Calanoida, Appendicularia, Chaetognatha and Decapoda species. The MinION proved to sequence with sufficient precision to allow for correct taxonomic assignment and the waiting time was considerably less than the MiSeq (sequencing results within 48 hours in-house versus 4-6 weeks outsourced, respectively). While the MinION was cost-effective for a preliminary, small sample-size study, on a larger scale the cost per sample would be comparable to the MiSeq.


Biography:

Aimee van der Reis is marine scientist and her research mainly focuses on using molecular tools to answer ecological questions. Her current work is focused on using DNA metabarcoding to investigate the diet of various species, which has included deep-sea lobsters, marine birds and fish.

Date

Mar 21 - 23 2022
Expired!