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

Dataset type: Genomic
Data released on August 04, 2017

Arulandhu AJ; Barreto Crespo MT; Birck M; Burns M; Costessi A; Duijsings D; Gaspar FB; Hagelaar R; Haynes E; Hochegger R; Holst-Jensen A; Prins TW; Rechenmann F; Scholtens IMJ; Staats M; Voorhuijzen MM; Klingl A; Lundberg L; Natale C; Niekamp H; Barbante A; Perri E; Rosec J; Seyfarth R; Sovova T; Moorleghem CV; Ruth Sv; 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

DOI10.5524/100330

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.

Additional details

Read the peer-reviewed publication(s):

Arulandhu, A. J., Staats, M., Hagelaar, R., Voorhuijzen, M. M., Prins, T. W., Scholtens, I., … Kok, E. (2017). Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples. GigaScience, 6(10), 1–18. doi:10.1093/gigascience/gix080

Additional information:

https://github.com/RIKILT/CITESspeciesDetect

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

Accessions (data included in GigaDB):

BioProject: PRJEB18620





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
S4_Lab_31427524  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:ERS1546558
Alternative accession-BioSample:SAMEA81332668
S4_Lab_41427524  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:ERS1546559
Alternative accession-BioSample:SAMEA81333418
S4_Lab_51427524  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:ERS1546560
Alternative accession-BioSample:SAMEA81334168
S4_Lab_61427524  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:ERS1546561
Alternative accession-BioSample:SAMEA81334918
S4_Lab_71427524  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:ERS1546562
Alternative accession-BioSample:SAMEA81335668
S4_Lab_81427524  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:ERS1546563
Alternative accession-BioSample:SAMEA81336418
S4_Lab_91427524  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:ERS1546564
Alternative accession-BioSample:SAMEA81337168
S5_Lab_11427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Triticum aestivum, 4% Aloe variegata, 4% Dendrobium sp., 4% Huso Dauricus, 4% Crocodylus niloticus, 41% Brassica oleracea and 41% Bos taurus, in dry weight percentages.
Alternative accession-SRA Sample:ERS1546572
Alternative accession-BioSample:SAMEA81343168
S5_Lab_101427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Triticum aestivum, 4% Aloe variegata, 4% Dendrobium sp., 4% Huso Dauricus, 4% Crocodylus niloticus, 41% Brassica oleracea and 41% Bos taurus, in dry weight percentages.
Alternative accession-SRA Sample:ERS1546581
Alternative accession-BioSample:SAMEA81349918
S5_Lab_111427524  mixed sample Description:Experimental mixture containing 1% Zea mays, 1% Triticum aestivum, 4% Aloe variegata, 4% Dendrobium sp., 4% Huso Dauricus, 4% Crocodylus niloticus, 41% Brassica oleracea and 41% Bos taurus, in dry weight percentages.
Alternative accession-SRA Sample:ERS1546582
Alternative accession-BioSample:SAMEA81350668
Displaying 91-100 of 177 Sample(s).




File NameSample IDData 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).
Funding body Awardee Award ID Comments
European Commission FP7-KBBE-2013-7-613908-Decathlon Seventh Framework Programme (FP7)

Protocols.io:

Date Action
August 4, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix080