Pricing – DNA Barcoding

All prices are in Canadian dollars and apply to submissions involving 96-well plates of tissues. This price schedule is based on the use of standard CCDB protocols and applies to all researchers and organizations.  Standard protocols may not be appropriate for all tissue types (e.g. older museum specimens or forensic samples) and additional charges may apply.
Go here for pricing of our other genomic and metagenomic services.

CCDB carries out the following steps:

  • CCDB Admin: Plate reception, specimen data validation, billing.
  • CCDB Analytical Lab: DNA extraction, PCR amplification of the barcode region(s), bidirectional amplicon sequencing (where applicable), trace file assembly, uploading trace files and sequences to BOLD.
  • BOLD Systems: Data validation and storage.

 



Analytical Services (Sanger Sequencing) Full Cost-Recovery* Barcode Library Contribution**
High-throughput barcode analysis1 (8×12 plate/box)
Animal tissue (single pass only) 2 $2,200.00 $1,250.00
Animal tissue (failure-tracking, optional) 3 $1,540.00 $875.00
Animal tissue (first pass with failure-tracking) 2+3 $3,750.00 $2,125.00
Animal tissue (older and/or degraded material) 4 $3,100.00 $1,750.00
Plant tissue 5 $3,300.00 $1,800.00
Fungal and algal tissue 6 $2,640.00 $1,500.00
Barcode Analysis with SMRT Sequencing on PacBio Sequel**,7 Price with SPRI DNA Extraction8 Price with GFP DNA Extraction9
Batch of 48 96-well plates (fresh material, insects only) $17,100.00 $22,800.00
Batch of 96 96-well plates (fresh material, insects only) $27,360.00 $38,760.00
Miscellaneous services (per 8×12 plate/box)
Voucher recovery and return 10 $300.00
Subsampling and tissue return 11 $250.00
DNA repatriation 12 $250.00
Additional marker 13 $1,000.00
Ultrahigh-throughput barcode analysis (4 @ 8×12) 14 Request a quote

Price Categories

* Full Cost-Recovery rate will apply to all submissions unless the Provider qualifies for the discounted rate (see below).

** Barcode Library Contribution rate is available to Providers that align their research efforts with our mission to assemble a DNA barcode library for all eukaryotic species. Barcode Library Contribution rate applies only to submissions where all required data elements are uploaded to BOLD. To qualify, Providers must conform to the following metadata quality standards: collection location with GPS co-ordinates, voucher specimen images (representative images are not acceptable), museum voucher location and ID and full taxonomy to the level of species or operational taxonomic unit. The Provider also must agree to data sharing in compliance with best practices established under iBOL Data Release Policy Phase 1 (Phase 2 data release will commence upon data publication but within five years from the date the sequence has been generated).

 

Analytical Services

1 Standard package to which additional services can be added. Please note that all submissions must follow the 96- well microplate guidelines available on our website. This high-throughput barcode analysis is available for animals (COI) 2, plants (matK+rbcL) 5 and fungi (ITS) 6 and includes the following services: Metadata validation, DNA extraction, PCR amplification, bidirectional sequencing of barcode regions(s), sequence assembly and base calling, and sequence and trace file upload to the Barcode of Life Database (BOLD).

2 Single pass barcode analysis of animal tissue is recommended for samples that are expected to yield high quality DNA. This service will involve single round of PCR with universal primers targeting full barcode region (658bp or similar length), followed by PCR check, and bidirectional sequencing. Quality of the provided material will impact the results and for poorly preserved and/or old specimens with degraded DNA additional analysis may be recommended. Results are normally available within 1-3 weeks from the date the lab begins processing of samples. Lead time depends on the size of the queue and can be extended due to missing or incomplete specimen data and/or payment delays.

3 Some samples may fail to amplify and/or sequence due to random primer mismatches or degraded material. Revisiting failed samples with primer sets that target shorter overlapping fragments spanning the barcode region enables barcode recovery. This option delays processing time significantly as the analysis must be completed in multiple stages. Allow additional 2-4 weeks to complete processing of samples.

4 Recommended for submissions with mostly old specimens that are not likely to produce amplicons for full barcode region. This option allows use of failure-tracking option as the initial step resulting in reduced processing time. Results are normally available within 2-3 weeks from the date the lab begins processing of samples.

5 This offer applies to plant tissues submitted in 96-tube racks. This option includes analysis of two markers (barcode standard for plants) with bidirectional sequencing, sequence editing and submission of traces and consensus sequences to BOLD.  Results are normally available within 2-4 weeks from the date the lab begins processing of samples.

6 This offer applies to fungal and algal specimens submitted in 96-tube racks. This option includes analysis of single loci (barcode standard for fungi or algae) with bidirectional sequencing, sequence editing and submission of traces and consensus sequences to BOLD. Results are normally available within 1-3 weeks from the date the lab begins processing of samples.

7 This high-throughput barcoding protocol includes DNA extraction from fresh tissue samples (or whole vouchers for small organisms) in a single batch of 96-well plates. Freshly extracted DNA is used as template for PCR amplification in 384-well format with CLepFol primer cocktails thus material must be fresh. This works well for most insects and other terrestrial arthropods. As the produced amplicons require pooling prior to SMRT sequencing workflow, each amplicon is dual-indexed with a unique pair of molecular tags (unique molecular identifier, UMI) on both 5′- and 3′-ends. The position of a sample in a 96-well plate and the place each 96-well plate occupies in the batch is used to link the unique pairs of UMIs in the resulting SMRT sequences to the source sample. The analysis of circular consensus sequences is supported by mBrave followed by validation and submission of results to BOLD. Because the indexing PCR requires the production of template-free PCR plates in large batches and in sets of 24 384 plates, and due to complexity of the workflow which involves five processing stages that collectively include 30 steps, we can only accept samples in batches of 48 or 96 plates. Based on the number of samples in a single batch (4560 or 9120) or DNA extraction protocol requested (SPRI or GFP), the price per sample ranges from $3.00 CAD to $5.00 CAD per specimen. Because the data analysis and validation take a lot more time, we aim to complete sample processing and deliver the results within 3-5 weeks provided there are no delays with specimen data and plate record submission.

8 CCDB introduced a SPRI DNA extraction protocol in 2019 as an alternative to the glass-fiber extraction method. While the SPRI method is more scalable, it is not suited for older material or samples with high polysaccharide contents (e.g. mollusks or echinoderms). As well, it does not tolerate oversampling so it is crucial to follow the sample submission requirements. Oversampling will result in poor DNA extraction and a subsequent failure to amplify the COI barcode region even in fresh specimens.

9 The analysis involves decade-proven automated CCDB glass fiber membrane protocol as a fail-proof alternative to the more sensitive SPRI method. Due to capacity constraints and higher consumable and labour cost, it is a more expensive option with longer pre-sequencing processing time.

 

Miscellaneous Services (Optional)

10 Voucher recovery and return: This service is recommended for submissions of very small or even tiny organisms (e.g. mites, ticks) where tissue sub-sampling is not feasible and whole organisms must be included in the initial stages of DNA extraction.

11 Subsampling and tissue return: All tissue sent for molecular analysis will be analyzed consumptively and no residual tissue will remain. This optional service overrides this policy. Tissue remains can be returned upon request.

12 DNA Return: Our policy is that all DNA extracts are retained for quality control purposes under the terms specified in the documents provided with the sample submission kit (BMTA/BMAA). This optional service overrides this policy.

13 Additional marker: DNA extracts are reprocessed with an additional, non-standard primer set. This service includes PCR amplification, bidirectional sequencing, sequence assembly & base calling, and sequence and trace file upload to the BOLD.

 

Ultrahigh-Throughput Barcode Analysis

14 We offer specialized 384-well analytical pipeline that was specifically designed for the analysis of arthropod samples collected in Malaise traps, but that can be employed to analyze terrestrial arthropods collected in other ways.  This analysis involves DNA extraction, PCR amplification and unidirectional sequence analysis and automated trace file analysis at extremely competitive rates, but is only available on studies examining 5000 or more specimens.

Contact us for a quote if your project will involve the analysis of more than 5000 specimens and will meet other criteria: applications@ccdb.ca

 

Special Services (R&D, Forensics, High-Throughput Sequencing (HTS))

Contact us for a quote if your project requires R&D or HTS: applications@ccdb.ca

For all other inquiries: info@ccdb.ca