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Creating, curating, and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA
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  • Emily Dziedzic,
  • Brian Sidlauskas,
  • Richard Cronn,
  • James Anthony,
  • Trevan Cornwell,
  • Thomas Friesen,
  • Peter Konstantinidis,
  • Brooke Penaluna,
  • Staci Stein,
  • Taal Levi
Emily Dziedzic
Oregon State University

Corresponding Author:[email protected]

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Brian Sidlauskas
Oregon State University
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Richard Cronn
USDA Forest Service Pacific Northwest Research Station
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James Anthony
Oregon Department of Fish and Wildlife
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Trevan Cornwell
Oregon Department of Fish and Wildlife
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Thomas Friesen
Oregon Department of Fish and Wildlife
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Peter Konstantinidis
Oregon State University
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Brooke Penaluna
USDA Forest Service Pacific Northwest Research Station
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Staci Stein
Oregon Department of Fish and Wildlife
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Taal Levi
Oregon State University
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Abstract

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon’s fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous, and estuarine fishes representing 24 families, 55 genera, and 128 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial “barcode” regions typically used for eDNA assays do not consistently diagnose for species, and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon’s fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences, and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
23 Feb 2023Submitted to Molecular Ecology Resources
27 Feb 2023Submission Checks Completed
27 Feb 2023Assigned to Editor
27 Feb 2023Review(s) Completed, Editorial Evaluation Pending
27 Feb 2023Reviewer(s) Assigned
17 Apr 2023Editorial Decision: Revise Minor
13 May 20231st Revision Received
18 May 2023Assigned to Editor
18 May 2023Submission Checks Completed
18 May 2023Review(s) Completed, Editorial Evaluation Pending
30 Jun 2023Editorial Decision: Revise Minor
11 Jul 20232nd Revision Received
13 Jul 2023Submission Checks Completed
13 Jul 2023Assigned to Editor
13 Jul 2023Review(s) Completed, Editorial Evaluation Pending
02 Aug 2023Editorial Decision: Accept