A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field

• Main Authors: Freitag, Hendrik, Maestri, Simone, Cosentino, Emanuela, Paterno, Marta, Garces, Jhoana M, Marcolungo, Luca, Alfano, Massimiliano, Njunjić, Iva, Schilthuizen, Menno, Slik, Ferry, Menegon, Michele, Rossato, Marzia, Delledonne, Massimo
• Format: text
• Published: Archīum Ateneo 2019
• Subjects: nanopore sequencing; long reads; field ecology; barcoding; portable lab; biodiversity; Biodiversity; Biology; Ecology and Evolutionary Biology
• Online Access: https://archium.ateneo.edu/biology-faculty-pubs/2; https://archium.ateneo.edu/cgi/viewcontent.cgi?article=1001&context=biology-faculty-pubs
• Institution: Ateneo De Manila University

Genetic markers (DNA barcodes) are often used to support and confirm species identification. Barcode sequences can be generated in the field using portable systems based on the Oxford Nanopore Technologies (ONT) MinION sequencer. However, to achieve a broader application, current proof-of-principle workflows for on-site barcoding analysis must be standardized to ensure a reliable and robust performance under suboptimal field conditions without increasing costs. Here, we demonstrate the implementation of a new on-site workflow for DNA extraction, PCR-based barcoding, and the generation of consensus sequences. The portable laboratory features inexpensive instruments that can be carried as hand luggage and uses standard molecular biology protocols and reagents that tolerate adverse environmental conditions. Barcodes are sequenced using MinION technology and analyzed with ONTrack, an original de novo assembly pipeline that requires as few as 1000 reads per sample. ONTrack-derived consensus barcodes have a high accuracy, ranging from 99.8 to 100%, despite the presence of homopolymer runs. The ONTrack pipeline has a user-friendly interface and returns consensus sequences in minutes. The remarkable accuracy and low computational demand of the ONTrack pipeline, together with the inexpensive equipment and simple protocols, make the proposed workflow particularly suitable for tracking species under field conditions.