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- U.S. Food and Drug Administration
- Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library
- DNA Barcodes: Methods and Protocols
U.S. Food and Drug Administration
Sara M. Handy and Jonathan R. Deeds U. Natalia V. Ivanova and Paul D. Andrea Ormos and Lee A. Michelle M. Moore U. Rosalee S. Hellberg U. Haile F.
Yancy U. A detailed single laboratory validated protocol is provided for DNA sequencing of the cytochrome c oxidase subunit I gene COI of seafood tissue samples for the purpose of obtaining unique, species-specific "barcodes" for species identification. This LIB is no longer available online. For additional information, contact Dr. Jonathan Deeds. Seafood is one of the most highly traded commodities in the world. In the interest of public health, it is vital that both domestically processed and imported seafood is safe, wholesome, and properly labeled.
To aid in the proper labeling of seafood, the Food and Drug Administration FDA maintains a list of acceptable market names for seafood sold in U. Organized in a series of species "pages," the RFE contains high resolution images of whole fish and their marketed product forms e.
An example of an identification method listed in the RFE is protein identification by isoelectric focusing 2. Isoelectric focusing is a currently accepted tool employed in the identification of fish fillets for regulatory compliance, but such analysis requires subjective interpretations of gel results and the inclusion of perishable frozen tissue standards in each run.
Further, the technique is not effective in the case of processed or cooked samples. The RFE was designed so that it could be expanded to include additional data and to accommodate the use of newer analytical tools as they became available.
Work is furthest advanced for members of the animal kingdom. In this case, a region of the cytochrome c oxidase subunit 1 gene COI has been targeted and pilot studies have shown its effectiveness in species identification.
The Fish Barcode of Life campaign FISH-BOL is a collaborative international research effort which seeks to establish a reference library of DNA barcodes for all fish species derived from voucher specimens with authoritative taxonomic identifications 4. Fishes comprise nearly half of all vertebrate species; the group includes approximately 15, marine and 13, freshwater species FishBase.
In , this protocol was evaluated by three laboratories in an inter-laboratory trial and the results of this trial were used to further refine the method. A step by step protocol based on this published SLV study, with minor modifications, is provided below. NOTE: Reference to any commercial materials, equipment, or process does not in any way constitute approval, endorsement, or recommendation by the Food and Drug Administration.
The process of generating DNA barcodes suitable for species identification from an unknown fish tissue sample can be broken down into the following steps:. Individual labs will likely modify this SOP based on available equipment and reagents.
In addition, for steps such as tissue lysis and DNA extraction, several commercial kits are available that may be acceptable. Any deviations from the described SOP will need to be proven to provide acceptable results. Performance criteria for individual steps are provided to aid in this process. A detailed SOP based on the single laboratory validation study detailed in Handy et al. Note: Only necessary if a subset is needed for long term storage, e.
Goal : Sample unknown fish tissues in a manner that prevents cross-contamination between samples, or the introduction of foreign DNA. Criteria for Success : After sequencing, have a chromatogram that gives single peaks for each base as evidenced by the AB1 file.
Each fish or fish fillet sampled should be bagged and labeled separately. Tissue samples should be removed with a scalpel and forceps that are flame sterilized after each sample is processed. New sterile tubes should be used for each sample. For long term storage of critical samples e. Each set of reactions also requires two negative controls, one which consists of the PCR cocktail with no additional DNA template added and another with an addition of the extraction negative control.
These samples have to be negative on the agarose gel no band produced. Goal : To produce an amplicon free of extra dNTPs and excess primers that might interfere with the sequencing reaction. Criteria for Success : Examine the PCR thermocycler to ensure that the run has completed at the correct temperatures and there are no error messages.
Criteria for success : Examine the thermocycler to ensure that the run has completed at the correct temperatures and there are no error messages. Goal : To remove unincorporated dye terminators and salts from sequencing reactions so that they will not interfere with the base pair determination of the fragment.
Several websites exist that are devoted to the troubleshooting of DNA sequencing. This is a helpful example from Etonbio. Criteria for Success : Generation of an AB1 file suitable for post sequencing analysis, though determination of the accurate base pair composition cannot be assessed until successful completion of Step 8: Post-Sequencing Analysis. Goal : To process the sequence from the AB1 file into a usable unit for comparison with sequences from a database of authenticated standards.
This database will be updated as more standards are added to the library. The database will be dated to distinguish it from previous versions. Analysts should check periodically to assure they are using the current database. In the event that a sequence from an unknown tissue sample does not match any sequence in the FDA database, the sequence can be screened against other publically available sources such as GenBank and BOLD.
These identifications should be considered presumptive unless the sequences were derived from specimens with proper authoritative taxonomic identification. FDA will only make regulatory decisions based on identifications using adequately authenticated standards. Inclusion of sequences from publically available databases should be noted in the analytical worksheet.
More elaborate statistical methods to define species boundaries are also available Kerr et al. For example, a character-based approach was recently used to successfully distinguish some of the closely related commercial species of tuna Lowenstein et al.
In some cases they can still be distinguished with this method, in other cases they cannot. Few examples exist in the FDA Seafood List where 2 closely related species that cannot be distinguished with this method have different approved market names.
Introduction Seafood is one of the most highly traded commodities in the world. Martin, Collette, and Slavin, eds. Official Method AOAC 63 ; corr. Food Prot. Fish Biol. It is no longer available. A single laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. Modifications from Handy et al. A Nalgene 2. Protocol for Tissue Sampling Goal : Sample unknown fish tissues in a manner that prevents cross-contamination between samples, or the introduction of foreign DNA.
Several tissues are suitable for DNA extraction from fishes. These include: Musculature preferred : remove one or more cubes mm of lateral muscle skin removed. Fin clips: remove fin rays and membrane from the pectoral or pelvic fin.
Use these tissues only if the fish needs to be kept alive. Eye: remove the right eye from extremely small specimens such as larvae. Buffer AL and ethanol can be premixed and added together in one step to save time when processing multiple samples. Mark the bottle to indicate that ethanol has been added. Buffer AL can be purchased separately if the same kit will be used for purification of DNA from animal blood.
Buffer AL is stable for 1 year after the addition of ethanol when stored closed at room temperature. Vortexing should be performed by pulse-vortexing for s. Include a negative extraction control with each set of extractions. The negative extraction control is treated exactly the same as sample tubes except that it does not contain any fish tissue. Vortex occasionally during incubation to disperse the sample, or place in a thermomixer, shaking water bath, or on a rocking platform.
Lysis time varies depending on the type of tissue processed. Lysis is usually complete in h. If it is more convenient, samples can be lysed overnight; this will not affect them adversely. After incubation the lysate may appear viscous, but should not be gelatinous as it may clog the DNeasy Mini spin column.
If the lysate appears very gelatinous, see the "Troubleshooting Guide", page 47, for recommendations. Vortex for 15 s. Add Then add It is essential that the sample, Buffer AL, and ethanol are mixed immediately and thoroughly by vortexing or pipetting to yield a homogeneous solution.
Note : A white precipitate may form on addition of Buffer AL and ethanol.
Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library
Sara M. Handy and Jonathan R. Deeds U. Natalia V. Ivanova and Paul D. Andrea Ormos and Lee A.
DNA Barcodes: Methods and Protocols
Detailed specimen data taxonomy, collection sites, and voucher catalogue numbers are available on BOLD under doi. Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg Germany to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. The 18 fish species were assigned to 20 molecular barcode index numbers, the aquatic invertebrate taxa to molecular entities.
DNA barcodes for soil animal taxonomy.