Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA
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 harne...
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| Published in | Molecular ecology resources Vol. 23; no. 8; pp. 1880 - 1904 |
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| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Wiley Subscription Services, Inc
01.11.2023
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| Abstract | 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 129 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. |
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| AbstractList | 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 129 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. 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 129 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. |
| Author | Friesen, Thomas A. Stein, Staci Cronn, Richard Cornwell, Trevan Anthony, James Penaluna, Brooke E. Sidlauskas, Brian Dziedzic, Emily Konstantinidis, Peter Levi, Taal |
| Author_xml | – sequence: 1 givenname: Emily orcidid: 0000-0002-5889-4110 surname: Dziedzic fullname: Dziedzic, Emily organization: Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA – sequence: 2 givenname: Brian orcidid: 0000-0003-0597-4085 surname: Sidlauskas fullname: Sidlauskas, Brian organization: Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA – sequence: 3 givenname: Richard surname: Cronn fullname: Cronn, Richard organization: Pacific Northwest Research Station, US Department of Agriculture Forest Service Corvallis Oregon USA – sequence: 4 givenname: James surname: Anthony fullname: Anthony, James organization: Oregon Department of Fish and Wildlife, Corvallis Research Laboratory Corvallis Oregon USA – sequence: 5 givenname: Trevan surname: Cornwell fullname: Cornwell, Trevan organization: Oregon Department of Fish and Wildlife, Corvallis Research Laboratory Corvallis Oregon USA – sequence: 6 givenname: Thomas A. surname: Friesen fullname: Friesen, Thomas A. organization: Oregon Department of Fish and Wildlife, Corvallis Research Laboratory Corvallis Oregon USA – sequence: 7 givenname: Peter surname: Konstantinidis fullname: Konstantinidis, Peter organization: Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA – sequence: 8 givenname: Brooke E. surname: Penaluna fullname: Penaluna, Brooke E. organization: Pacific Northwest Research Station, US Department of Agriculture Forest Service Corvallis Oregon USA – sequence: 9 givenname: Staci surname: Stein fullname: Stein, Staci organization: Oregon Department of Fish and Wildlife, Corvallis Research Laboratory Corvallis Oregon USA – sequence: 10 givenname: Taal orcidid: 0000-0003-1853-8311 surname: Levi fullname: Levi, Taal organization: Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA |
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Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence... Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence... |
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| SubjectTerms | Bats Biodiversity Comparative analysis Environmental DNA Freshwater fish Genera Genomics Taxa |
| Title | Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA |
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