Development of specific markers for the detection of Tolypella canadensis eDNA in water samples
Assessing the biodiversity of an ecosystem plays a major role in ecosystem management. However, proper determination on species-level is often tricky when morphological features are scarce and especially rare species require huge sampling efforts to be detected in the aquatic realm. As an alternativ...
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2021
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ftzenodo:oai:zenodo.org:4599995 2024-09-15T18:39:10+00:00 Development of specific markers for the detection of Tolypella canadensis eDNA in water samples Wiebe, Christina Nowak, Petra Schubert, Hendrik 2021-03-04 https://doi.org/10.3897/aca.4.e64932 unknown Pensoft Publishers https://doi.org/10.3897/aca.4.e64932 oai:zenodo.org:4599995 info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode ARPHA Conference Abstracts, 4, e64932, (2021-03-04) Tolypella canadensis Characeae eDNA genetic marker ITS2 info:eu-repo/semantics/article 2021 ftzenodo https://doi.org/10.3897/aca.4.e64932 2024-07-26T19:54:23Z Assessing the biodiversity of an ecosystem plays a major role in ecosystem management. However, proper determination on species-level is often tricky when morphological features are scarce and especially rare species require huge sampling efforts to be detected in the aquatic realm. As an alternative to conventional methods, environmental samples can be examined via the eDNA method, allowing for large-scale integration as well as taxa resolution independent from expression of morphological characters. However, to apply this technique genetic markers that are specific to a species or at least a genus are required. Such markers until now have been successfully developed only for a few well studied taxonomic groups like, e.g., fishes and amphibians, but are still missing for others, especially plants and algae (e.g. Bista et al. 2017). This project focusses on the development of species-specific markers for the macrophytic green algae Tolypella canadensis (Characeae, Charophyta), a rare alga preferring deep water and known so far mainly from remote places. Tolypella canadensis is a circumpolar species and prefers oligotrophic lakes, where it grows in depths up to 13 m (Langangen 2002; Romanov and Kopyrina 2016). In addition, proper determination of Tolypella-species is a field of a few specialists, further complicating monitoring or even detection of this rare species. The design of the species-specific primers was based on reference nucleotide sequences of the chloroplast genes rbc L, psb C and atp B and of the ribosomal internal transcribed spacer regions ITS1 and ITS2, obtained from GenBank (Perez et al. 2017). To determine the specificity of the newly designed primers, DNA isolates obtained from T. canadensis specimens collected from the Torneträsk (Sweden, 2018) and other charophyte species were prepared in different proportions. The sensitivity of the primers was experimentally assayed by using serial dilutions of T. canadensis DNA. Additionally, a mock test comprised of a sample with the DNA of several ... Article in Journal/Newspaper Tolypella canadensis Zenodo ARPHA Conference Abstracts 4 |
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Tolypella canadensis Characeae eDNA genetic marker ITS2 |
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Tolypella canadensis Characeae eDNA genetic marker ITS2 Wiebe, Christina Nowak, Petra Schubert, Hendrik Development of specific markers for the detection of Tolypella canadensis eDNA in water samples |
topic_facet |
Tolypella canadensis Characeae eDNA genetic marker ITS2 |
description |
Assessing the biodiversity of an ecosystem plays a major role in ecosystem management. However, proper determination on species-level is often tricky when morphological features are scarce and especially rare species require huge sampling efforts to be detected in the aquatic realm. As an alternative to conventional methods, environmental samples can be examined via the eDNA method, allowing for large-scale integration as well as taxa resolution independent from expression of morphological characters. However, to apply this technique genetic markers that are specific to a species or at least a genus are required. Such markers until now have been successfully developed only for a few well studied taxonomic groups like, e.g., fishes and amphibians, but are still missing for others, especially plants and algae (e.g. Bista et al. 2017). This project focusses on the development of species-specific markers for the macrophytic green algae Tolypella canadensis (Characeae, Charophyta), a rare alga preferring deep water and known so far mainly from remote places. Tolypella canadensis is a circumpolar species and prefers oligotrophic lakes, where it grows in depths up to 13 m (Langangen 2002; Romanov and Kopyrina 2016). In addition, proper determination of Tolypella-species is a field of a few specialists, further complicating monitoring or even detection of this rare species. The design of the species-specific primers was based on reference nucleotide sequences of the chloroplast genes rbc L, psb C and atp B and of the ribosomal internal transcribed spacer regions ITS1 and ITS2, obtained from GenBank (Perez et al. 2017). To determine the specificity of the newly designed primers, DNA isolates obtained from T. canadensis specimens collected from the Torneträsk (Sweden, 2018) and other charophyte species were prepared in different proportions. The sensitivity of the primers was experimentally assayed by using serial dilutions of T. canadensis DNA. Additionally, a mock test comprised of a sample with the DNA of several ... |
format |
Article in Journal/Newspaper |
author |
Wiebe, Christina Nowak, Petra Schubert, Hendrik |
author_facet |
Wiebe, Christina Nowak, Petra Schubert, Hendrik |
author_sort |
Wiebe, Christina |
title |
Development of specific markers for the detection of Tolypella canadensis eDNA in water samples |
title_short |
Development of specific markers for the detection of Tolypella canadensis eDNA in water samples |
title_full |
Development of specific markers for the detection of Tolypella canadensis eDNA in water samples |
title_fullStr |
Development of specific markers for the detection of Tolypella canadensis eDNA in water samples |
title_full_unstemmed |
Development of specific markers for the detection of Tolypella canadensis eDNA in water samples |
title_sort |
development of specific markers for the detection of tolypella canadensis edna in water samples |
publisher |
Pensoft Publishers |
publishDate |
2021 |
url |
https://doi.org/10.3897/aca.4.e64932 |
genre |
Tolypella canadensis |
genre_facet |
Tolypella canadensis |
op_source |
ARPHA Conference Abstracts, 4, e64932, (2021-03-04) |
op_relation |
https://doi.org/10.3897/aca.4.e64932 oai:zenodo.org:4599995 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.3897/aca.4.e64932 |
container_title |
ARPHA Conference Abstracts |
container_volume |
4 |
_version_ |
1810483562115235840 |