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Data released on November 03, 2017

Supporting data for "Filling reference gaps via assembling DNA barcodes using high-throughput sequencing - moving toward barcoding the world"

Liu, S; Yang, C; Zhou, C; Zhou, X (2017): Supporting data for "Filling reference gaps via assembling DNA barcodes using high-throughput sequencing - moving toward barcoding the world" GigaScience Database. http://dx.doi.org/10.5524/100363 RIS BibTeX Text

Over the past decade, biodiversity scientists have dedicated tremendous efforts in constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2,000, further dramatic reduction on barcoding costs is unlikely because the Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also refrained High-Throughput-Sequencing (HTS) based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length COI barcodes from pooled PCR amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from over 78% of the PCR reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform, Pacbio, confirmed the accuracy the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about 1/10 of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix104

Additional information:

https://github.com/comery/HIFI-barcode-hiseq

https://github.com/comery/HIFI-barcode-pacbio

dx.doi.org/10.17504/protocols.io.ka9csh6

Accessions (data included in GigaDB):

BioProject: PRJNA414137

Keywords:

dna-barcoding high-throughput sequencing coi pcr gap-filling 

Genomic, Metabarcoding

http://gigadb.org/images/data/cropped/100363.jpg

Funding:

  • Funding body - Chinese Universities Scientific Fund
  • Award ID - 2017QC114
  • Awardee - X Zhou

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
hifi01-B091248154  Neptis alwina Description:COI gene amplified from genomic DNA ex...
Species-a:Neptis alwina
Sample collection device or method:Malaise trap
...
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hifi01-B10224126  Stichophthalma howqua Description:COI gene amplified from genomic DNA ex...
Species-a:Stichophthalma howqua
Sample collection device or method:Malaise trap
...
+
hifi01-B111430627  Phthonosema tendinosaria Description:COI gene amplified from genomic DNA ex...
Species-a:Phthonosema tendinosaria
Sample collection device or method:Malaise trap
...
+
hifi01-B12441321  Colias fieldii Description:COI gene amplified from genomic DNA ex...
Species-a:colias fieldii fieldii
Sample collection device or method:Malaise trap
...
+
hifi01-C011974491  Aporia genestieri Description:COI gene amplified from genomic DNA ex...
Species-a:Aporia genestieri pseudopotanini
Sample collection device or method:Malaise trap
...
+
hifi01-C0250557 true insectsInsecta Description:COI gene amplified from genomic DNA ex...
Species-a:Oxyambulyx ochracea
Sample collection device or method:Malaise trap
...
+
hifi01-C0350557 true insectsInsecta Description:COI gene amplified from genomic DNA ex...
Species-a:Limbatochlamys parvisis
Sample collection device or method:Malaise trap
...
+
hifi01-C047088mothsbutterflies and mothsLepidoptera Description:COI gene amplified from genomic DNA ex...
Species-a:Ephesia helena
Sample collection device or method:Malaise trap
...
+
hifi01-C0550557 true insectsInsecta Description:COI gene amplified from genomic DNA ex...
Species-a:Insect
Sample collection device or method:Malaise trap
...
+
hifi01-C0676196  Papilio protenor Description:COI gene amplified from genomic DNA ex...
Species-a:Papilio protenor protenor
Sample collection device or method:Malaise trap
...
+
Displaying 21-30 of 192 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 
Sequence assemblyFASTA62.65 KB2017-10-16
Sequence assemblyFASTA68.34 KB2017-10-16
TextTEXT2.13 MB2017-10-16
AlignmentsFASTA13.03 MB2017-10-16
OtherFASTA7.01 MB2017-10-16
Amplicon sequenceFASTQ332.74 MB2017-10-16
Amplicon sequenceFASTQ381.34 MB2017-10-16
Amplicon sequenceFASTQ288.24 MB2017-10-16
Amplicon sequenceFASTQ351.5 MB2017-10-16
TextUNKNOWN0.18 KB2017-10-16
Displaying 1-10 of 23 File(s).

History:

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