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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; Hagelaar, R; Staats, M; Voorhuijzen, M, M; Prins, T, W; Scholtens, I, M; Costessi, A; Duijsings, D; Rechenmann, F; Gaspar, F, B; Barreto Crespo, M, T; Holst-Jensen, A; Birck, M; Burns, M; Haynes, E; Hochegger, R; Klingl, A; Lundberg, L; Natale, C; Niekamp, H; Perri, E; Barbante, A; 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

Additional information:

https://github.com/RIKILT/CITESspeciesDetect

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

Protocols.io:

https://www.protocols.io/widgets/protocol/development-and-validation-of-a-multi-locus-dna-me-ixbcfin

Accessions (data included in GigaDB):

BioProject: PRJEB18620

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_141427524  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:ERS1546553
Alternative accession-BioSample:SAMEA81328918
S3_Lab_151427524  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:ERS1546554
Alternative accession-BioSample:SAMEA81329668
S3_Lab_161427524  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:ERS1546555
Alternative accession-BioSample:SAMEA81330418
S3_Lab_21427524  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:ERS1546541
Alternative accession-BioSample:SAMEA81319918
S3_Lab_31427524  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:ERS1546542
Alternative accession-BioSample:SAMEA81320668
S3_Lab_41427524  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:ERS1546543
Alternative accession-BioSample:SAMEA81321418
S3_Lab_51427524  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:ERS1546544
Alternative accession-BioSample:SAMEA81322168
S3_Lab_61427524  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:ERS1546545
Alternative accession-BioSample:SAMEA81322918
S3_Lab_71427524  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:ERS1546546
Alternative accession-BioSample:SAMEA81323668
S3_Lab_81427524  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:ERS1546547
Alternative accession-BioSample:SAMEA81324418
Displaying 71-80 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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