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Data released on August 04, 2017

Supporting data for "Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples"

Arulandhu, A, J; Barreto Crespo, M, T; Birck, M; Burns, M; Costessi, A; Duijsings, D; Gaspar, F, B; Hagelaar, R; Haynes, E; Hochegger, R; Holst-Jensen, A; Prins, T, W; Rechenmann, F; Scholtens, I, M; Staats, M; Voorhuijzen, M, M; Klingl, A; Lundberg, L; Natale, C; Niekamp, H; Barbante, A; Perri, E; Rosec, J; Seyfarth, R; Sovova, T; Moorleghem, C, V; Ruth, S, V; Peelen, T; Kok, E (2017): Supporting data for "Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples" GigaScience Database. http://dx.doi.org/10.5524/100330 RIS BibTeX Text

DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa, and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.

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Related manuscripts:

doi:10.1093/gigascience/gix080

Additional information:

https://github.com/RIKILT/CITESspeciesDetect

http://decathlon-fp7.citespipe-wur.surf-hosted.nl:8080/

Protocols.io:

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Accessions (data included in GigaDB):

BioProject: PRJEB18620

Keywords:

Endangered species CITES Traditional medicines DNA metabarcoding Customs agencies COI matK rbcL cyt b mini-barcodes 

Genomic

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Funding:

  • Funding body - European Commission
  • Award ID - FP7-KBBE-2013-7-613908-Decathlon
  • Comment - Seventh Framework Programme (FP7)

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
S3_Lab_91427524  mixed sample Description:Traditional medicine with the following ingredients on the label: Herba Cistanches, Cauda cervi, Radix Rehmanniae praeparata, Radix Ginseng, Radix morindae Officinalis, Semen Cuscutae, Radix Achyranthis bidentatae, Rhizoma Cibotii, Semen Platycladi, Cortex Eucommiae, Radix Astragali, Fructus Schisandrae chinensis, Cortex Cinnamomi and Cornu Cervi Pantotrichum
Alternative accession-SRA_sample:ERS1546548
Alternative accession-BioSample:SAMEA81325168
S4_Lab_11427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546556
Alternative accession-BioSample:SAMEA81331168
S4_Lab_101427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546565
Alternative accession-BioSample:SAMEA81337918
S4_Lab_111427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546566
Alternative accession-BioSample:SAMEA81338668
S4_Lab_121427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546567
Alternative accession-BioSample:SAMEA81339418
S4_Lab_131427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546568
Alternative accession-BioSample:SAMEA81340168
S4_Lab_141427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546569
Alternative accession-BioSample:SAMEA81340918
S4_Lab_151427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546570
Alternative accession-BioSample:SAMEA81341668
S4_Lab_161427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546571
Alternative accession-BioSample:SAMEA81342418
S4_Lab_21427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Brassica napus, 3% Aloe variegata, 3% Dendrobium sp., 3% Huso Dauricus, 3% Crocodylus niloticus, 43% Brassica oleracea and 43% Bos taurus, in dry weight percentages.
Alternative accession-SRA_sample:ERS1546557
Alternative accession-BioSample:SAMEA81331918
Displaying 81-90 of 177 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
GitHub archivearchive13.58 MB2017-07-28
S5_Lab_5Tabular dataTSV7.83 KB2017-07-28
S5_Lab_5Tabular dataTSV4.97 KB2017-07-28
S5_Lab_5Tabular dataTSV8.55 KB2017-07-28
S5_Lab_5Tabular dataTSV8.11 KB2017-07-28
S5_Lab_5Tabular dataTSV0.81 KB2017-07-28
S5_Lab_5Tabular dataTSV7.63 KB2017-07-28
S5_Lab_5Tabular dataTSV14.48 KB2017-07-28
S5_Lab_5Tabular dataTSV15.1 KB2017-07-28
S5_Lab_5Tabular dataTSV14.63 KB2017-07-28
Displaying 1-10 of 14 File(s).

History:

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