Improving Environmental DNA Sensitivity for Dreissenid Mussels by Targeting Tandem Repeat Regions of the Mitochondrial Genome

Abstract

The recent genetic revolution through the analysis of aquatic environmental DNA (eDNA) has become a powerful tool for improving the detection of rare and/or invasive species. For the majority of eDNA studies, genetic assays are designed to target mitochondrial genes commonly referred to as “barcode” regions. However, unlike the typical structure of an animal mitochondrial genome, those for the invasive zebra and quagga mussels are greatly expanded with large extended tandem repeat regions. These sections of repeated DNA can appear hundreds of times within the genome compared to a single copy for the mitochondrial barcode genes. This higher number of target copies per mitochondrial genome presents an opportunity to increase eDNA assay sensitivity for these species. Therefore, we designed and evaluated new eDNA assays to target the extended repeat sections for both zebra and quagga mussels. These assays lower the limit of detection of genomic DNA by 100-fold for zebra mussels and 10-fold for quagga mussels. Additionally, these newly developed assays provided longer durations of detection during degradation mesocosm experiments and greater sensitivity for eDNA detection from water samples collected across western Lake Erie compared to standard assays targeting mitochondrial genes. This work illustrates how understanding the complete genomic structure of an organism can improve eDNA analysis.

Mussels on the move: new records of the invasive non-native quagga mussel (Dreissena rostriformis bugensis) in Great Britain using eDNA and a new probe-based qPCR assay

“…Moreover, the LOD obtained for the pDRB1 assay in this study was 100 copies/µL. While Blackman et al (2020b) had previously reported a LOD of 1E-04 ng/μL for the dDRB1 assay with SYBR green dye, and Marshall, Vanderploeg & Chaganti (2022) found the LOD to be 9.8E-05 ng/reaction for the same assay with the EvaGreen dye, the different units used to assess limits of detection (ng/μL and copies/μL) makes the direct comparison between LODs not fair.…”