Fahner, N. | Search bioRxiv

bioRxiv2023

NAMERS: a purpose-built reference DNA sequence database to support applied eDNA metabarcoding

Applied eDNA metabarcoding is increasingly being used to generate actionable results to inform management decisions, regulations, or policy development. Because of these important downstream considerations, optimizing workflow elements is now essential to increasing standardization, efficiency, and confidence of metabarcoding results. Reference DNA sequences are critical workflow elements that currently lack consistent approaches to generating, curating, or publishing. Here we present a complete (mitochondrial genome and nuclear ribosomal DNA cistron) and high quality reference DNA sequence library for the freshwater fishes of British Columbia, Canada. This resource is published as the Novel Applied eDNA Metabarcoding Reference Sequences (NAMERS) repository (https://namers.ca), a user-friendly and interactive website for specialists and non-specialists alike to explore and generate custom reference libraries for taxa and genes of interest. We demonstrate the power of NAMERS to optimize applied eDNA metabarcoding workflows at the study design stage by analyzing the number of primer mismatches and resolution power of existing metabarcoding markers. To meet the increasing demand for actionable eDNA metabarcoding applications, NAMERS demonstrates that high quality curated genomic information is within a reasonable reach. It is timely to establish this framework as the new gold standard and coordinate our efforts to generate this type of reference data at scale.

genetics↗

bioRxiv2020

The utility of a metagenomics approach for marine biomonitoring

1The isolation and analysis of environmental DNA (eDNA) for ecosystem assessment and monitoring has become increasingly popular. A majority of studies have taken a metabarcoding approach--that is, amplifying and sequencing one or more gene targets of interest. Shotgun sequencing of eDNA--also called metagenomics--while popular in microbial community analysis has not seen much adoption for the analysis of other groups of organisms. Especially in light of the existence of extremely high-capacity DNA sequencers, we decided to test the performance of a shotgun approach side-by-side with a metabarcoding approach on marine water samples obtained from offshore Newfoundland. We found that metabarcoding remains the most efficient technique, but that metagenomics also has significant power to reveal biodiversity patterns, and in fact can be treated as an independent confirmation of ecological gradients. Moreover, we show that metagenomics can also be used to infer factors related to ecosystem health and function.

ecology↗