On site DNA barcoding by nanopore sequencing

Abstract

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.

Coral reef ecosystem functioning: eight core processes and the role of biodiversity

“…For instance, rapid, non‐lethal on‐site DNA barcoding with nanopore sequencing (Menegon et al . ) or metabarcoding of environmental DNA (eDNA) now offer scope for high‐resolution inventories of reef communities (DiBattista et al . ).…”

“…However, emerging molecular techniques provide new tools for describing lesser-known reef taxa. For instance, rapid, non-lethal on-site DNA barcoding with nanopore sequencing (Menegon et al 2017) or metabarcoding of environmental DNA (eDNA) now offer scope for high-resolution inventories of reef communities (DiBattista et al 2017). Where species-level identifications cannot be achieved, groupings along phylogenetic or functional boundaries are an alternative (Freeman et al 2014;Madin et al 2016).…”

Three new minute leaf litter beetles discovered by citizen scientists in Maliau Basin, Malaysian Borneo (Coleoptera: Leiodidae, Chrysomelidae)

“…Under the guidance of embedded taxonomists, the participants identify and describe new taxa belonging to the taxonomists' field of expertise. The collected materials are stored in a local collection and provided with voucher numbers that are referred to in all output such as published taxonomic treatments, web-based taxonomy platforms, and 3rd-generation DNA sequencing of DNA barcodes in the field (Menegon et al 2017). …”

Dispatch from the field II: the mystery of the red and blue Opadometa male (Araneae, Tetragnathidae, Opadometa sarawakensis)

“…For an unplanned field discovery such as this one, arranging for sequencing at a domestic institution requires time and resources beyond the scope of this study. Technologies for DNA barcoding in the field appear tantalizingly close to practicality and one of us (MS with Taxon Expeditions) is involved with field trials of the MinION, a portable DNA sequencer from Oxford Nanopore Technologies (Menegon et al 2017). We hope to see more successful DNA sequencing under field conditions in the near future, but for now, we will have to be content with non-molecular (e.g., behavioral and faunistic) lines of evidence for sex matching in remote field studies.…”