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Short COI markers for freshwater macroinvertebrate metabarcoding

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104 days ago
RT @VascoElbrecht: @PeerJPreprints @owenwangensteen @EvaAylagas @leeselab @MBMGjournal = ) Feedback and reviews were really helpful! Articl…
@PeerJPreprints @owenwangensteen @EvaAylagas @leeselab @MBMGjournal = ) Feedback and reviews were really helpful! Article will be available @MBMGjournal soon (Preprint already online; https://t.co/MBhZz2Rn3P)
RT @metabar_papers: Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/fun5k8ovkM
RT @metabar_papers: Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/fun5k8ovkM
Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/fun5k8ovkM
RT @luckylionde: @MikiBalint @mailys_gauthier @leeselab Yes, those are the short ones here https://t.co/MBhZz38Ysp. Did you use the fwhR2n…
@MikiBalint @mailys_gauthier @leeselab Yes, those are the short ones here https://t.co/MBhZz38Ysp. Did you use the fwhR2n version Mailys? The fwhR2 is not so good (design error)
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
140 days ago
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
RT @PeerJPreprints: New Preprint: "Short COI markers for freshwater macroinvertebrate metabarcoding" https://t.co/fCokrjq03R
147 days ago
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
New Preprint: "Short COI markers for freshwater macroinvertebrate metabarcoding" https://t.co/fCokrjq03R
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
150 days ago
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
151 days ago
RT @luckylionde: New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https…
151 days ago
RT @metabar_papers: Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/2SdWxoWL7H
151 days ago
RT @metabar_papers: Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/2SdWxoWL7H
New freshwater #macrozoobenthos #primers online! Optimised for degraded DNA, #eDNA #metabarcoding -> @PeerJPreprints https://t.co/MBhZz38Ysp https://t.co/3PYNlkqZWg
152 days ago
Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/fRbE9vhkQz
RT @metabar_papers: Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/2SdWxoWL7H
Short COI markers for freshwater macroinvertebrate metabarcoding https://t.co/2SdWxoWL7H
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Supplemental Information

Suppl. material 1 - Table S1

Primers evaluated in this study

DOI: 10.7287/peerj.preprints.3037v2/supp-1

Suppl. material 2: Figure S1

Developed fusion primers for fwh1 and fwh2 on the Illumina high throughput sequencing platform.

DOI: 10.7287/peerj.preprints.3037v2/supp-2

Suppl. material 3: Figure S2

Overview of similarity of used inline tags for the fwh1 and fwh2 fusion primers.

DOI: 10.7287/peerj.preprints.3037v2/supp-3

Suppl. material 4: Table S2

Overview of the three Romanian macrozoobenthos sampling sites (Z2, L2, R2).

DOI: 10.7287/peerj.preprints.3037v2/supp-4

Suppl. material 5: Figure S3

Overview of the macroinvertebrates composition of the three sample sites in Romania.

DOI: 10.7287/peerj.preprints.3037v2/supp-5

Suppl. material 6: Table S3

Overview of used tagging combinations for sample multiplexing for sequencing.

DOI: 10.7287/peerj.preprints.3037v2/supp-6

Suppl. material 7: Figure S4

Gradient PCR optimisation for the fwh primer sets.

DOI: 10.7287/peerj.preprints.3037v2/supp-7

Suppl. material 8: Script S1

JAMP metabarcoding pipeline (used R commands).

DOI: 10.7287/peerj.preprints.3037v2/supp-8

Suppl. material 9: Figure S5

Number of raw sequences obtained for each sample after demultiplexing.

DOI: 10.7287/peerj.preprints.3037v2/supp-9

Suppl. material 10: Table S4

OTU table for the 52 taxa mock samples sequenced with the fwh1 and fwh2 primer set.

DOI: 10.7287/peerj.preprints.3037v2/supp-10

Suppl. material 11: Figure S6

Proportion of shared reads between the two replicates for DceM amplified with the fwh1 primer set.

DOI: 10.7287/peerj.preprints.3037v2/supp-11

Suppl. material 12: Figure S7

Sample composition of Romanian macroinvertebrate samples.

DOI: 10.7287/peerj.preprints.3037v2/supp-12

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Ecaterina Edith Vamos conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

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

Florian Leese conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Raw sequencing data is available on NCBI SRA (SRR5295658 and SRR5295659).

Funding

EV was supported by a fellowship of the Dr. Musat V. Bodnarescu foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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