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Transitioning from environmental genetics to genomics using mitogenome reference databases
  • +7
  • 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:emily.dziedzic@oregonstate.edu

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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 the 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 complete mitogenomic sequence information to evaluate the effectiveness of such data to differentiate, identify and detect taxa. We created the Oregon Biodiversity Genome Project working group to utilize recent advances in sequencing technology to create a database of complete, near error-free mitogenomic sequences for all of Oregon’s resident freshwater fishes. So far, we have successfully assembled the complete mitogenomes of 313 specimens of freshwater fish representing 7 families, 55 genera, and 129 (88%) of the 146 resident species and lineages. Our comparative analyses of these sequences illustrate that the short (~150 bp) mitochondrial “barcode” regions typically used for eDNA assays are not consistently diagnostic for species-level identification and that no single region is best for metabarcoding Oregon’s fishes. However, often-overlooked intergenic regions of the mitogenome such as the D-loop have the potential to reliably diagnose and differentiate species. This project provides a blueprint for other researchers to follow as they build regional databases. It also illustrates the taxonomic value and limits of complete mitogenomic sequences, and how current eDNA assays and the “PCR-free” environmental genomics methods of the future can best leverage this information.