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Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring

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RT @VascoElbrecht: The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features…
RT @VascoElbrecht: The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features…
RT @VascoElbrecht: The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features…
RT @metabar_papers: Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/QQmAWHZj9i
RT @VascoElbrecht: The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features…
RT @metabar_papers: Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/QQmAWHZj9i
RT @metabar_papers: Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/QQmAWHZj9i
RT @metabar_papers: Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/QQmAWHZj9i
RT @VascoElbrecht: The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features…
RT @metabar_papers: Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/QQmAWHZj9i
RT @VascoElbrecht: The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features…
104 days ago
RT @VascoElbrecht: The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features…
The updated @PeerJPreprints of our #macroinvertebrate #metabarcodign paper is online (https://t.co/tIDCoCc29e)! Features a slightly improved workflow, and great feedback from @BerndHaenfling. Thank you = ) Maybe soon accepted at Freshwater Biology
104 days ago
Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/wIyl1C5yrl
Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring https://t.co/QQmAWHZj9i
Just submitted the updated preprint as well = ) should be available tomorrow. But for every one who can't wait, here is the slightly older version https://t.co/tIDCoCc29e
RT @VascoElbrecht: @eDNAScience @QIAGEN @dirch3 @BraukmannThomas @BiodiversityIn1 Thanks :D very happy with the 96 plate extractions and pc…
@eDNAScience @QIAGEN @dirch3 @BraukmannThomas @BiodiversityIn1 Thanks :D very happy with the 96 plate extractions and pcr. There is actually a sophisticated sample layout behind this, allowing to detect contamination and other things that might go wrong. See @PeerJPreprints: https://t.co/tIDCoCtDxO ☺️
@KristenFerns Maybe you find this video helpful concerning fusion primer design : ) https://t.co/k6q0EMdfW6 here is also the related @PeerJPreprints https://t.co/tIDCoCtDxO please let me know if i can help with anything #metabarcoding related : )
Getting things ready for 96 well plate extractions! =) Will use single tubes for digestions as the powder does too quickly disperse by static charging. But then switching to @Quiagen plate extractions after that. Scaling up #metabarcoding! @PeerJPreprints: https://t.co/tIDCoCc29e https://t.co/HhxiKqIBCV
@Gnarly_Larvae @dirch3 Yes, that’s probably the reason. The fusion primer system works brilliantly with 5% phiX, heterogeneity spacers (also used at in-line barcodes), and parallel sequencing. See also https://t.co/tIDCoCtDxO for recommendations : ) please let me know if you have any questions!
Hundreds of grinding chambers have arrived and @QIAGEN plate extraction kits for #metabarcoding at large scale! More information on scaling things up, here: https://t.co/tIDCoCc29e https://t.co/ZmCTAj0ZJh
A bit more shifting has to be done till for the 21 #metabarcoding primer sets to be tagged and tested = ) A Levenshtein distance of 1-2 bp means the primers are too similar -> Tagswitching can happen! scripts and more info in this related @PeerJPreprints: https://t.co/tIDCoCc29e https://t.co/KOm08QCFWL
RT @VascoElbrecht: Update of our scaling up #metabarcoding @PeerJPreprints is online! =) some minor improvements + new example sample layou…
218 days ago
RT @VascoElbrecht: Update of our scaling up #metabarcoding @PeerJPreprints is online! =) some minor improvements + new example sample layou…
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"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Supplemental Information

Figure S1: Newly developed fusion primer sets (BF2+BR2), suitable for tagging 288 individual wells

DOI: 10.7287/peerj.preprints.3456v5/supp-1

Figure S2: Base composition of the inline tagging region

DOI: 10.7287/peerj.preprints.3456v5/supp-2

Figure S3: Hamming distance between tags for all fusion primers

DOI: 10.7287/peerj.preprints.3456v5/supp-3

Figure S4: Levenshtein distance between tags for all fusion primers

DOI: 10.7287/peerj.preprints.3456v5/supp-4

Script S1: R script used for randomly generating inline barcodes for the given primer sets (includes visualization, as shown in Figure S3 and Figure 3)

DOI: 10.7287/peerj.preprints.3456v5/supp-5

Table S1: Table providing an overview of proposed tagging combinations (as shown in Figure 3)

DOI: 10.7287/peerj.preprints.3456v5/supp-6

Manuscript file for providing feedback

(Pleas use track changes)

DOI: 10.7287/peerj.preprints.3456v5/supp-7

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Vasco Elbrecht conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Dirk Steinke authored or reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

Primer sequences and scripts to generated them are provided as supporting information.

Funding

V.E. and D.S. are supported by funding through the Canada First Research Excellence Fund. This work represents a contribution to the ‘Food From Thought’ research program and the EU Action ‘DNAqua-Net’ (CA15219). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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