| Abstract Detail
Conservation Biology Harbert, Robert [1]. Monitoring plant biodiversity in aquatic eDNA with low-cost Nanopore Flongle sequencing. Premise of the study – Cellular and cell-free DNA obtained from environmental samples of soil, water, and air can detect local biodiversity. Environmental DNA (eDNA) sequencing typically relies on standard molecular techniques and resources. Here we present a fully portable workflow designed to work with limited infrastructure for the collection, isolation, extraction, sequencing, and analysis of aquatic eDNA for the monitoring of plant biodiversity.
Methods – DNA was extracted from aquatic eDNA from an open pond and a seasonal wetland. Samples were amplified targeting 350bp to 890bp segments from psbA3, rbcLa, ITS2, 18S, trnL genomic regions. Amplified DNA was barcoded, pooled up to twelve reactions per run, and sequenced on the Oxford Nanopore MinION sequencer using the low-throughput Flongle flowcells. Amplicon sequences were classified using Kraken2 and BLAST followed by a lowest common ancestor algorithm using the NCBI taxonomy.
Results – eDNA sequencing reveals highly local differences in plant diversity including both aquatic and terrestrial taxa.
Discussion – The workflow built around this platform provides end-to-end amplicon-based sequencing that can be used to detect nearby plant diversity. The Oxford Nanopore MinION sequencer and the low throughput Flongle flowcell provides a sequencing platform that combines portability, low-cost, and ease of use that are essential features for field applications of amplicon metabarcoding.
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Analysis development repository
Protocol
1 - Stonehill College, Biology, 320 Washington St., North Easton, MA, 02357, United States
Keywords:
eDNA
metabarcoding
biodiversity
nanopore.
Presentation Type: Poster
Session: P1, Conservation Biology Posters
Location: Virtual/Virtual
Date: Monday, July 19th, 2021
Time: 5:00 PM(EDT)
Number: P1CB001
Abstract ID:65
Candidate for Awards:None |
