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Are Genetic Reference Libraries Sufficient for Environmental DNA Metabarcoding of Mekong River Basin Fish?

Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
Department of Biology and Global Water Center, University of Nevada, Reno, NV 89557, USA
Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, CA 93106, USA
Wonders of the Mekong Project, c/o Inland Fisheries Research and Development Institute, Fisheries Administration, No. 186, Preah Norodom Blvd., Khan Chamcar Morn, P.O. Box 582, Phnom Penh 12300, Cambodia
Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
Mekong River Commission Secretariat, P.O. Box 6101, 184 Fa Ngoum Road, Unit 18, Vientiane 01000, Laos
Cambodia National Mekong Committee, No. 576, National Road No. 2, Sangkat Chak Angre Krom, Khan Meanchey, Phnom Penh 12300, Cambodia
Author to whom correspondence should be addressed.
Academic Editor: José Maria Santos
Water 2021, 13(13), 1767;
Received: 16 May 2021 / Revised: 15 June 2021 / Accepted: 16 June 2021 / Published: 26 June 2021
Environmental DNA (eDNA) metabarcoding approaches to surveillance have great potential for advancing biodiversity monitoring and fisheries management. For eDNA metabarcoding, having a genetic reference sequence identified to fish species is vital to reduce detection errors. Detection errors will increase when there is no reference sequence for a species or when the reference sequence is the same between different species at the same sequenced region of DNA. These errors will be acute in high biodiversity systems like the Mekong River Basin, where many fish species have no reference sequences and many congeners have the same or very similar sequences. Recently developed tools allow for inspection of reference database coverage and the sequence similarity between species. These evaluation tools provide a useful pre-deployment approach to evaluate the breadth of fish species richness potentially detectable using eDNA metabarcoding. Here we combined established species lists for the Mekong River Basin, resulting in a list of 1345 fish species, evaluated the genetic library coverage across 23 peer-reviewed primer pairs, and measured the species specificity for one primer pair across four genera to demonstrate that coverage of genetic reference libraries is but one consideration before deploying an eDNA metabarcoding surveillance program. This analysis identifies many of the eDNA metabarcoding knowledge gaps with the aim of improving the reliability of eDNA metabarcoding applications in the Mekong River Basin. Genetic reference libraries perform best for common and commercially valuable Mekong fishes, while sequence coverage does not exist for many regional endemics, IUCN data deficient, and threatened fishes. View Full-Text
Keywords: eDNA; sequencing; species richness; biodiversity eDNA; sequencing; species richness; biodiversity
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MDPI and ACS Style

Jerde, C.L.; Mahon, A.R.; Campbell, T.; McElroy, M.E.; Pin, K.; Childress, J.N.; Armstrong, M.N.; Zehnpfennig, J.R.; Kelson, S.J.; Koning, A.A.; Ngor, P.B.; Nuon, V.; So, N.; Chandra, S.; Hogan, Z.S. Are Genetic Reference Libraries Sufficient for Environmental DNA Metabarcoding of Mekong River Basin Fish? Water 2021, 13, 1767.

AMA Style

Jerde CL, Mahon AR, Campbell T, McElroy ME, Pin K, Childress JN, Armstrong MN, Zehnpfennig JR, Kelson SJ, Koning AA, Ngor PB, Nuon V, So N, Chandra S, Hogan ZS. Are Genetic Reference Libraries Sufficient for Environmental DNA Metabarcoding of Mekong River Basin Fish? Water. 2021; 13(13):1767.

Chicago/Turabian Style

Jerde, Christopher L., Andrew R. Mahon, Teresa Campbell, Mary E. McElroy, Kakada Pin, Jasmine N. Childress, Madeline N. Armstrong, Jessica R. Zehnpfennig, Suzanne J. Kelson, Aaron A. Koning, Peng Bun Ngor, Vanna Nuon, Nam So, Sudeep Chandra, and Zeb S. Hogan. 2021. "Are Genetic Reference Libraries Sufficient for Environmental DNA Metabarcoding of Mekong River Basin Fish?" Water 13, no. 13: 1767.

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