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Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

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RT @aimz_vdReis: Newest version of my pre-print is available & touches on what to consider before doing a full metabarcoding study, i.e. wh…
Newest version of my pre-print is available & touches on what to consider before doing a full metabarcoding study, i.e. what difference do DNA polymerases make? @PeerJPreprints https://t.co/cRgDIScZgG #Aquaculture #Fisheries #Bioinformatics #Genetics #Metabarcoding
138 days ago
Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding https://t.co/DKj6wCyvoo
Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding https://t.co/DvfcnCiz1k
Interested how important sequencing different genes can change you metabarcoding results? @PeerJPreprints https://t.co/cRgDIScZgG #AquacultureFisheriesandFishScience #Bioinformatics #Genetics #metabarcoding #molecularbiology #NZscampi #COI #18SrRNA #MarineBiology
RT @aimz_vdReis: A prelim of what NZ scampi eat - @PeerJPreprints https://t.co/cRgDIScZgG #AquacultureFisheriesandFishScience #Bioinformat…
250 days ago
Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding https://t.co/rWWqQAEjhA
Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding https://t.co/TAhMifg9kr
RT @aimz_vdReis: A prelim of what NZ scampi eat - @PeerJPreprints https://t.co/cRgDIScZgG #AquacultureFisheriesandFishScience #Bioinformat…
A prelim of what NZ scampi eat - @PeerJPreprints https://t.co/cRgDIScZgG #AquacultureFisheriesandFishScience #Bioinformatics #Genetics
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Supplemental Information

PCR profile designed for the optimum DNA amplification using either the COI or 18S primers

(A) Initial denaturation at 95 °C for 60 seconds. (B) 20 “touch-up” cycles, with each cycle having a denaturation step at 95 °C for 30 seconds, an annealing step starting at 45 °C for 30 seconds (each annealing cycle increases 1 °C every cycle) and a final extension step at 72 °C for 30 seconds. (C) 20 “touch-down” cycles, with each cycle having a denaturation step at 95 °C for 30 seconds, an annealing step starting at 65 °C for 30 seconds (each annealing cycle decreases 1 °C every cycle) and a final extension step at 72 °C for 30 seconds. (D) 10 cycles, with each cycle having a denaturation step at 95 °C for 15 seconds, an annealing step at 45 °C for 20 seconds and a final extension step at 72 °C for 30 seconds. (E) Final extension cycle at 72 °C for 60 seconds and holding at 15 °C.

DOI: 10.7287/peerj.preprints.26667v2/supp-1

Platinum Taq reaction

Reagent volumes and concentrations used in a 25 μl Platinum Taq reaction.

DOI: 10.7287/peerj.preprints.26667v2/supp-2

Bioline reaction

Reagent volumes and concentrations used in a 25 μl Bioline reaction.

DOI: 10.7287/peerj.preprints.26667v2/supp-3

Processed reads for COI and 18S

Resulting totals for paired, merged and cleaned reads for COI and 18S.

DOI: 10.7287/peerj.preprints.26667v2/supp-4

The DNA concentration and purity ratios per individual for each digesta source

Nucleic acids have strong absorbance at 260 nm, which is also the wavelength where purines and pyrimidines peak. At 280 nm, proteins and phenolic compounds have a strong absorbance. A wavelength of 230 nm is known to absorb organic compounds. Pure DNA should ideally be 1.8 for A260/A280 and close to 2.0 for A260/A230 (Watts 2014).

DOI: 10.7287/peerj.preprints.26667v2/supp-5

COI diet reads

COI genus reads were filtered from the COI cleaned reads and then categorized into DNA negative reads, lobster and/or terrestrial reads and diet reads.

DOI: 10.7287/peerj.preprints.26667v2/supp-6

18S diet reads

18S genus reads were filtered from the 18S cleaned reads and then categorized into DNA negative reads, lobster and/or terrestrial reads and diet reads.

DOI: 10.7287/peerj.preprints.26667v2/supp-7

Taxa identified as diet taxa (genus and/or species level) from the COI databases

The taxa are separated into their OTUs with their assigned taxonomic identity, hit counts, Midori RDP confidence levels, NCBI e-values and grouping.

DOI: 10.7287/peerj.preprints.26667v2/supp-8

COI diet sequences

COI OTUs and assigned sequences (genus and/or species level).

DOI: 10.7287/peerj.preprints.26667v2/supp-9

Taxa identified as diet taxa (genus and/or species level) from the 18S databases

The taxa are separated into their OTUs with their assigned taxonomic identity, hit counts, SILVA RDP confidence levels, PR2 RDP confidence levels, NCBI e-values and grouping.

DOI: 10.7287/peerj.preprints.26667v2/supp-10

18S diet sequences

18S OTUs and assigned sequences (genus and/or species level).

DOI: 10.7287/peerj.preprints.26667v2/supp-11

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Aimee L van der Reis conceived and designed the experiments, performed 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.

Olivier Laroche contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Andrew G Jeffs conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft, oversaw logistics and administration.

Shane D Lavery conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

Specimens for this study were collected in accordance with approvals under New Zealand’s Animal Welfare Act 1991. The transport and holding of the scampi, as well as the experimental procedures, were approved by the Animal Ethics Committee of the Nelson Marlborough Institute of Technology (AEC2014-CAW-02).

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

New Zealand’s Ministry of Primary Industries - Special Permit #549

DNA Deposition

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

The sequences of the scampi diet matching genus/species have been uploaded as a supplemental file. Table S8 are the COI sequences and Table S10 are the 18S sequences.

Data Deposition

The following information was supplied regarding data availability:

Figshare

https://figshare.com/s/7724ecca36796209abf4

Funding

This study is part of ‘Ka Hao te Rangatahi: Revolutionary Potting Technologies and Aquaculture for Scampi’ (CAWX1316) funded by the New Zealand Ministry of Business Innovation and Employment. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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