Visitors   Views   Downloads

Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers

View preprint
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
RT @metabar_papers: Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular marker…
Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers https://t.co/SaNhLiPmFn We developed a metabarcoding method for biodiversity characterization of structurally complex natural marine hard-bottom com…
RT @owenwangensteen: After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set p…
18 days ago
Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers https://t.co/6JP60ph9nl
Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers https://t.co/xvjsvvBj7K
After 1.5 years drifting away in the Straits of Closed-Access Journals, we have finally sent our Leray-XT primer set paper to @PeerJPreprints for everyone to see. https://t.co/lm0TiV95P8 #Biodiversity #Ecology #MarineBiology
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Supplemental Information

Sequence logos for the novel COI Leray-XT primer set

DOI: 10.7287/peerj.preprints.3429v1/supp-2

Read abundances (mean + se) of MOTUs assigned to different taxonomic ranks using COI or 18S

DOI: 10.7287/peerj.preprints.3429v1/supp-3

Patterns of abundance of metabarcoding reads per replicate sample

Results presented for COI (upper graph) or 18S (lower graph) in eight different marine littoral communities from NE Atlantic (left) and W Mediterranean (right), and a set of lagoon sediment samples.

DOI: 10.7287/peerj.preprints.3429v1/supp-4

Patterns of relative MOTU richness obtained using COI (upper graph) or 18S (lower graph) from the same replicate samples of fig. S4

DOI: 10.7287/peerj.preprints.3429v1/supp-5

Pie charts showing the reproducibility of metabarcoding results

Plots correspond to three ecological replicates (upper row), three DNA extraction replicates (middle row) and three PCR replicates (lower row) for COI (left) and 18S (right). Arrows indicate which replicate is used in the next level of study.

DOI: 10.7287/peerj.preprints.3429v1/supp-6

nMDS plots showing the ordination patterns of Bray-Curtis dissimilarities calculated from read abundances (fourth root transformed)

Data correspond to all MOTUs detected in eight different marine littoral communities and a set of sediment samples from a tidal lagoon. The size fractions (A, B and C) are indicated. Analyses from COI (left) and 18S (right) are shown.

DOI: 10.7287/peerj.preprints.3429v1/supp-7

Summary of the metabarcoding pipelines for 18S and COI.

DOI: 10.7287/peerj.preprints.3429v1/supp-8

Summary of reference sequences included in the databases used for taxonomic assignment of COI and 18S with ecotag.

DOI: 10.7287/peerj.preprints.3429v1/supp-9

Final dataset for 18S, including sequences of all MOTUs, their taxonomic assignment and their abundances in each sample

DOI: 10.7287/peerj.preprints.3429v1/supp-10

Final dataset for COI, including sequences of all MOTUs, their taxonomic assignment and their abundances in each sample

DOI: 10.7287/peerj.preprints.3429v1/supp-11

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Owen S Wangensteen conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Creu Palacín performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Magdalena Guardiola performed the experiments, analyzed the data, reviewed drafts of the paper.

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

DNA Deposition

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

The sequences and accompanying information have been deposited in the Mendeley data repository (https://data.mendeley.com/datasets/nm2c97fjng/1)

Data Deposition

The following information was supplied regarding data availability:

The resulting datasets for COI and 18S, including sequences, taxonomic assignment and abundances for all MOTUs in every sample, have been deposited in the Mendeley data repository (https://data.mendeley.com/datasets/nm2c97fjng/1). Databases of reference sequences to be used for ecotag taxonomic assignment of COI and 18S are deposited in Github (http://github.com/metabarpark/Reference-databases). R scripts used as part of the analysis pipeline are also deposited in Github (http://github.com/metabarpark/R_scripts_metabarpark)

Funding

This work has been funded by projects Metabarpark from the Spanish National Parks Autonomous Agency (OAPN project 1036-2013) and ChallenGen CTM2013-48163 from the Spanish Government. OSW is currently funded by project SeaDNA, NE/N005759/1 grant from the Natural Environment Research Council (NERC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies