Prioritizing taxa for genetic reference database development to advance inland water conservation

Monchamp, Marie‐Ève; Taranu, Zofia E.; Garner, Rebecca E.; Rehill, Tessa; Morissette, Olivier; Iversen, Lars; Fugère, Vincent; Littlefair, Joanne E.; Costa, Naíla Barbosa da; Desforges, Jessica E.; Schacht, Joe R. Sánchez; Derry, Alison M.; Cooke, Steven J.; Barrett, Rowan D. H.; Walsh, David A.; Ragoussis, Jiannis; Albert, Monique; Cristescu, Melania E.; Gregory‐Eaves, Irene

doi:10.1016/j.biocon.2023.109963

Cited by 6 publications

(1 citation statement)

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“…Combining short‐ and long‐strand sequencing of environmental metagenomes may also be an alternative, allowing thorough investigation of fragmented and thus poorly preserved DNA from the sediments, but can be costly and time‐consuming (Pedersen et al, 2016). Importantly, all these methods are dependent upon adequate DNA sequence resources and reference databases (Monchamp et al, 2023). Overall, further research is required to meet ecological and methodological challenges, but in the meantime, it is essential to consolidate best practices from existing workflows to enable higher success in detecting fish DNA from sediment samples.…”

Section: Troubleshooting Fish Seddna Workflowsmentioning

confidence: 99%

Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities

Huston,

Lopez,

Cheng

et al. 2023

Environmental DNA

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Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short‐ and long‐term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro‐organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.

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Section: Troubleshooting Fish Seddna Workflowsmentioning

confidence: 99%