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Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples

Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale s...

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Autores principales: Jensen, Mads Reinholdt, Sigsgaard, Eva Egelyng, Liu, Shenglin, Manica, Andrea, Bach, Steffen Sanvig, Hansen, Michael Møller, Møller, Peter Rask, Thomsen, Philip Francis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7983877/
https://www.ncbi.nlm.nih.gov/pubmed/33179423
http://dx.doi.org/10.1111/1755-0998.13293
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author Jensen, Mads Reinholdt
Sigsgaard, Eva Egelyng
Liu, Shenglin
Manica, Andrea
Bach, Steffen Sanvig
Hansen, Michael Møller
Møller, Peter Rask
Thomsen, Philip Francis
author_facet Jensen, Mads Reinholdt
Sigsgaard, Eva Egelyng
Liu, Shenglin
Manica, Andrea
Bach, Steffen Sanvig
Hansen, Michael Møller
Møller, Peter Rask
Thomsen, Philip Francis
author_sort Jensen, Mads Reinholdt
collection PubMed
description Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA‐based population studies. The mitochondrial target capture successfully retrieved ~235× (90× − 352× per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant nontarget species, mackerel tuna (Euthynnus affinis), showing a clear relationship between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only a few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from E. affinis. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and nontarget sequences as well as presence of nontarget species at the sampling site, is crucial to consider. eDNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.
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spelling pubmed-79838772021-03-24 Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples Jensen, Mads Reinholdt Sigsgaard, Eva Egelyng Liu, Shenglin Manica, Andrea Bach, Steffen Sanvig Hansen, Michael Møller Møller, Peter Rask Thomsen, Philip Francis Mol Ecol Resour RESOURCE ARTICLES Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA‐based population studies. The mitochondrial target capture successfully retrieved ~235× (90× − 352× per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant nontarget species, mackerel tuna (Euthynnus affinis), showing a clear relationship between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only a few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from E. affinis. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and nontarget sequences as well as presence of nontarget species at the sampling site, is crucial to consider. eDNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species. John Wiley and Sons Inc. 2020-11-27 2021-04 /pmc/articles/PMC7983877/ /pubmed/33179423 http://dx.doi.org/10.1111/1755-0998.13293 Text en © 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle RESOURCE ARTICLES
Jensen, Mads Reinholdt
Sigsgaard, Eva Egelyng
Liu, Shenglin
Manica, Andrea
Bach, Steffen Sanvig
Hansen, Michael Møller
Møller, Peter Rask
Thomsen, Philip Francis
Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
title Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
title_full Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
title_fullStr Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
title_full_unstemmed Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
title_short Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
title_sort genome‐scale target capture of mitochondrial and nuclear environmental dna from water samples
topic RESOURCE ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7983877/
https://www.ncbi.nlm.nih.gov/pubmed/33179423
http://dx.doi.org/10.1111/1755-0998.13293
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