Supporting data for "Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment".

Dataset type: Imaging, Metabarcoding
Data released on September 14, 2015

Drummond AJ; Newcomb RD; Buckley TR; Xie D; Dopheide A; Potter BCM; Heled J; Ross HA; Tooman L; Grosser S; Park D; Demetras NJ; Stevens MI; Russell JC; Anderson SH; Carter A; Nelson N (2015): Supporting data for "Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment". GigaScience Database. http://dx.doi.org/10.5524/100144

DOI10.5524/100144

There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specialists for identification and only evaluate small subsets of biodiversity. Environmental DNA (eDNA) approaches are being promoted as a solution to these limitations, but questions remain unresolved. Here we evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life. We compare these data to traditional biodiversity monitoring tools, including mist-netting and call counts for birds, vegetation surveys, and invertebrate collection with DNA barcoding. Our sampling regime consisted of ten 20 × 20 metre plots, each comprising sixteen 5 × 5 metre sub-plots along a 700 metre elevational gradient on a temperate island forest ecosystem.
Across five molecular markers (16S, 18S, ITS, COI and trnL) we collected 3,537,908 sequence reads. From six eDNA data sets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 65 NCBI taxonomy-define phyla or equivalent high-level taxa, ranging from 12 (ITS) to 34 phyla (18S) for a given eDNA marker.

Additional details

Read the peer-reviewed publication(s):

Drummond, A. J., Newcomb, R. D., Buckley, T. R., Xie, D., Dopheide, A., Potter, B. C., … Nelson, N. (2015). Evaluating a multigene environmental DNA approach for biodiversity assessment. GigaScience, 4(1). doi:10.1186/s13742-015-0086-1

Additional information:

https://github.com/walterxie/eDNA-pipeline

Accessions (data included in GigaDB):

BioProject: PRJNA267737





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Plot 1-B410658Soil Metagenome soil metagenome PH:6.08
PH method:http://trove.nla.gov.au/version/42620262
Electrical Conductivity(EC):0.175865
...
+
Plot 1-L410658Soil Metagenome soil metagenome PH:6.41
PH method:http://trove.nla.gov.au/version/42620263
Electrical Conductivity(EC):0.248508
...
+
Plot 2-C410658Soil Metagenome soil metagenome PH:4.82
PH method:http://trove.nla.gov.au/version/42620264
Electrical Conductivity(EC):0.127402
...
+
Plot 2-M410658Soil Metagenome soil metagenome PH:4.95
PH method:http://trove.nla.gov.au/version/42620265
Electrical Conductivity(EC):0.103172
...
+
Plot 3-H410658Soil Metagenome soil metagenome PH:5.1
PH method:http://trove.nla.gov.au/version/42620266
Electrical Conductivity(EC):0.106448
...
+
Plot 3-N410658Soil Metagenome soil metagenome PH:5.13
PH method:http://trove.nla.gov.au/version/42620267
Electrical Conductivity(EC):0.161249
...
+
Plot 4-A410658Soil Metagenome soil metagenome PH:6.24
PH method:http://trove.nla.gov.au/version/42620268
Electrical Conductivity(EC):0.52014
...
+
Plot 4-N410658Soil Metagenome soil metagenome PH:5.72
PH method:http://trove.nla.gov.au/version/42620269
Electrical Conductivity(EC):0.671482
...
+
Plot 5-I410658Soil Metagenome soil metagenome PH:5.34
PH method:http://trove.nla.gov.au/version/42620270
Electrical Conductivity(EC):0.22083
...
+
Plot 5-N410658Soil Metagenome soil metagenome PH:5.74
PH method:http://trove.nla.gov.au/version/42620271
Electrical Conductivity(EC):0.13669
...
+
Displaying 1-10 of 20 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherCSV841.6 KB2015-06-02
OtherFASTA623.07 KB2015-06-02
16S rRNAFASTA4.61 MB2015-06-02
BLASTUNKNOWN4.18 GB2015-06-02
OtherUNKNOWN23.39 MB2015-06-02
OtherCSV360.95 KB2015-06-02
OtherFASTA66.9 KB2015-06-02
Coding sequenceFASTA1.98 MB2015-06-02
BLASTUNKNOWN2.21 GB2015-06-02
OtherUNKNOWN8.25 MB2015-06-02
Displaying 1-10 of 44 File(s).
Date Action
September 14, 2015 Dataset publish
September 14, 2015 Title updated from : Supporting data for "Evaluating a multigene environmental DNA approach for comprehensive biodiversity assessment".
June 13, 2016 Manuscript Link added : 10.1186/s13742-015-0086-1