Raw cutadapt miseq output - minibarcode 18S-V7 of macroalgae ...
Macroalgae are key primary producers in North Atlantic and Arctic coastal ecosystems, and tracing their fate and distribution is vital to improve our understanding of their ecological role and provision of ecosystem services. Recent advances from environmental DNA (eDNA) have added a new capacity to...
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| Format: | Dataset |
| Language: | English |
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Dryad
2021
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| Online Access: | https://dx.doi.org/10.5061/dryad.1jwstqjw9 https://datadryad.org/stash/dataset/doi:10.5061/dryad.1jwstqjw9 |
| Summary: | Macroalgae are key primary producers in North Atlantic and Arctic coastal ecosystems, and tracing their fate and distribution is vital to improve our understanding of their ecological role and provision of ecosystem services. Recent advances from environmental DNA (eDNA) have added a new capacity to fingerprint and trace macroalgae. However, further development of resources for amplifying and identifying macroalgal eDNA are much needed. Here, we examined the performance in terms of resolution and specificity of two 18S primers (18S-V7 & 18S-V9) recently applied in identifying macroalgae from eDNA. We also built a local barcode database for primer 18S-V7 with 31 widespread Arctic and North Atlantic macroalgal species to complement the existing DNA databases. Furthermore, we applied metabarcoding of eDNA to identify macroalgae in Arctic marine sediments (Disko Bay, W. Greenland) and evaluated the contributions from our local barcode database. We identified macroalgal DNA from 19 families across 11 orders ... : To develop the barcode database, macroalgal samples were collected along the coast of Denmark and Southwest and East Greenland in connection with various research expeditions (Table 1). The samples include 44 individuals (37 species) of red, green, and brown algae. Macroalgal tissue was homogenized using liquid nitrogen and grinded with a mortar and pestle, which were sterilized between samples with 10% bleach and 70% ethanol. DNA from 100 mg of grinded sample was extracted with the Nucleospin Plant II kit (Macherey-Nagel) following the manufacturers protocol. We targeted the 18S rDNA using the 18S-V7 primer pair (Table 3). PCR reactions contained 5 μl of QIAGEN Multiplex PCR Master Mix, 1 μl (1.0 μM) of each primer, 1 μl of DNA template, and 2 μl of PCR water. The PCR protocol for 18S-V7 was followed as detailed in table 3. A PCR blank with DNAfree water and a mock sample, with a mix of algal DNA samples in different DNA concentrations (Appendix B, table B1) was included with the samples. PCR amplicons were ... |
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