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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.

Contact Submitter

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
EM_11427524  mixed sample Description:Experimental mixture containing 99% Bos taurus and 1% Lactuca sativa
Alternative accession-SRA_sample:ERS1545972
Alternative accession-BioSample:SAMEA80893168
EM_101427524  mixed sample Description:Experimental mixture containing 10% Bos taurus, 10% Parapenaeopsis sp., 10% Anguilla anguilla, 10% Crocodylus niloticus, 10% Gallus gallus domesticus, 10% Pieris brassicae, 10% Echinocactus sp., 10% Euphorbia sp., 10% Aloe variegata, 10% Dendrobium sp., 10% Cycas revoluta and 10% Lactuca Sativa
Alternative accession-SRA_sample:ERS1545981
Alternative accession-BioSample:SAMEA80899918
EM_10R1427524  mixed sample Description:Experimental mixture containing 10% Bos taurus, 10% Parapenaeopsis sp., 10% Anguilla anguilla, 10% Crocodylus niloticus, 10% Gallus gallus domesticus, 10% Pieris brassicae, 10% Echinocactus sp., 10% Euphorbia sp., 10% Aloe variegata, 10% Dendrobium sp., 10% Cycas revoluta and 10% Lactuca Sativa
Alternative accession-SRA_sample:ERS1545982
Alternative accession-BioSample:SAMEA80900668
EM_111427524  mixed sample Description:Experimental mixture containing 46% Bos taurus, 1% Parapenaeopsis sp., 1% Anguilla anguilla, 1% Crocodylus niloticus, 1% Gallus gallus domesticus, 1% Pieris brassicae, 1% Echinocactus sp., 1% Euphorbia sp., 1% Aloe variegata, 1% Dendrobium sp., 1% Cycas revoluta and 46% Lactuca Sativa
Alternative accession-SRA_sample:ERS1545983
Alternative accession-BioSample:SAMEA80901418
EM_11R1427524  mixed sample Description:Experimental mixture containing 46% Bos taurus, 1% Parapenaeopsis sp., 1% Anguilla anguilla, 1% Crocodylus niloticus, 1% Gallus gallus domesticus, 1% Pieris brassicae, 1% Echinocactus sp., 1% Euphorbia sp., 1% Aloe variegata, 1% Dendrobium sp., 1% Cycas revoluta and 46% Lactuca Sativa
Alternative accession-SRA_sample:ERS1545984
Alternative accession-BioSample:SAMEA80902168
EM_121427524  mixed sample Description:Experimental mixture containing 95% Bos taurus, 1% Echinocactus sp., 1% Euphorbia sp., 1% Aloe variegata, 1% Dendrobium sp. and 1% Cycas revoluta
Alternative accession-SRA_sample:ERS1545985
Alternative accession-BioSample:SAMEA80902918
EM_131427524  mixed sample Description:Experimental mixture containing 85% Bos taurus, 3% Echinocactus sp., 3% Euphorbia sp., 3% Aloe variegata, 3% Dendrobium sp. and 3% Cycas revoluta
Alternative accession-SRA_sample:ERS1545986
Alternative accession-BioSample:SAMEA80903668
EM_141427524  mixed sample Description:Experimental mixture containing 1% Parapenaeopsis sp., 1% Anguilla anguilla, 1% Crocodylus niloticus, 1% Gallus gallus domesticus, 1% Pieris brassicae and 95% Lactuca sativa
Alternative accession-SRA_sample:ERS1545987
Alternative accession-BioSample:SAMEA80904418
EM_151427524  mixed sample Description:Experimental mixture containing 3% Parapenaeopsis sp., 3% Anguilla anguilla, 3% Crocodylus niloticus, 3% Gallus gallus domesticus, 3% Pieris brassicae and 85% Lactuca sativa
Alternative accession-SRA_sample:ERS1545988
Alternative accession-BioSample:SAMEA80905168
EM_21427524  mixed sample Description:Experimental mixture containing 90% Bos taurus and 10% Lactuca sativa
Alternative accession-SRA_sample:ERS1545973
Alternative accession-BioSample:SAMEA80893918
Displaying 1-10 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 
S5_Lab_5imageJPG164.51 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 dataTSV15.1 KB2017-07-28
S5_Lab_5Tabular dataTSV14.48 KB2017-07-28
S5_Lab_5Tabular dataTSV14.63 KB2017-07-28
S5_Lab_5Tabular dataTSV2.8 KB2017-07-28
Displaying 1-10 of 14 File(s).

History:

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