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Geographically widespread swordfish barcode stock identification: a case study of its application.

Pappalardo AM, Guarino F, Reina S, Messina A, De Pinto V - PLoS ONE (2011)

Bottom Line: This information was successfully applied to the discrimination of unknown samples from the market, detecting in some cases mislabeled seafood products.Similar results were obtained with 5'dloop.Our preliminary data in swordfish Xiphias gladius confirm that Cytochrome Oxidase I can be proposed as an efficient species-specific marker that has also the potential to assign geographical provenance.

View Article: PubMed Central - PubMed

Affiliation: Section of Biochemistry and Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, National Institute of Biomembranes and Biosystems, Section of Catania, Catania, Italy.

ABSTRACT

Background: The swordfish (Xiphias gladius) is a cosmopolitan large pelagic fish inhabiting tempered and tropical waters and it is a target species for fisheries all around the world. The present study investigated the ability of COI barcoding to reliably identify swordfish and particularly specific stocks of this commercially important species.

Methodology: We applied the classical DNA barcoding technology, upon a 682 bp segment of COI, and compared swordfish sequences from different geographical sources (Atlantic, Indian Oceans and Mediterranean Sea). The sequences of the 5' hyper-variable fragment of the control region (5'dloop), were also used to validate the efficacy of COI as a stock-specific marker.

Case report: This information was successfully applied to the discrimination of unknown samples from the market, detecting in some cases mislabeled seafood products.

Conclusions: The NJ distance-based phenogram (K2P model) obtained with COI sequences allowed us to correlate the swordfish haplotypes to the different geographical stocks. Similar results were obtained with 5'dloop. Our preliminary data in swordfish Xiphias gladius confirm that Cytochrome Oxidase I can be proposed as an efficient species-specific marker that has also the potential to assign geographical provenance. This information might speed the samples analysis in commercial application of barcoding.

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Parsimony network analysis of (A) the 16 COI swordfish haplotypes and (B) the 36 5′dloop haplotypes.Each connection represents one mutational step; small circles represent unsampled haplotypes. The size of each haplotype node is proportional to the number of specimens representing each haplotype. The total number of specimens in this network is 65. The network was generated using TCS 1.21 (available at http://darwin.uvigo.es/software/tcs.html) at the default 95% connection limit.
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pone-0025516-g003: Parsimony network analysis of (A) the 16 COI swordfish haplotypes and (B) the 36 5′dloop haplotypes.Each connection represents one mutational step; small circles represent unsampled haplotypes. The size of each haplotype node is proportional to the number of specimens representing each haplotype. The total number of specimens in this network is 65. The network was generated using TCS 1.21 (available at http://darwin.uvigo.es/software/tcs.html) at the default 95% connection limit.

Mentions: The NJ phenograms were supported by the parsimony network analyses that produced one haplotype group from COI sequences (Fig. 3A) and several for the 5′dloop sequences (Fig. 3B). In particular, Fig. 3A shows that H10 is the most common haplotype, shared between Indian and Atlantic Oceans. Mediterranean haplotypes H1, H2, H3, H5, H6, H15 are separated from H10 by two mutational steps (G-426-A and C-285-T) that represent their nucleotide diagnostics (ND) [22]. Another group of Mediterranean haplotypes (H4, H7, H8, H9) is connected with the Atlantic haplotype H12 and with the H10, that appears as most common haplotype.


Geographically widespread swordfish barcode stock identification: a case study of its application.

Pappalardo AM, Guarino F, Reina S, Messina A, De Pinto V - PLoS ONE (2011)

Parsimony network analysis of (A) the 16 COI swordfish haplotypes and (B) the 36 5′dloop haplotypes.Each connection represents one mutational step; small circles represent unsampled haplotypes. The size of each haplotype node is proportional to the number of specimens representing each haplotype. The total number of specimens in this network is 65. The network was generated using TCS 1.21 (available at http://darwin.uvigo.es/software/tcs.html) at the default 95% connection limit.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3198442&req=5

pone-0025516-g003: Parsimony network analysis of (A) the 16 COI swordfish haplotypes and (B) the 36 5′dloop haplotypes.Each connection represents one mutational step; small circles represent unsampled haplotypes. The size of each haplotype node is proportional to the number of specimens representing each haplotype. The total number of specimens in this network is 65. The network was generated using TCS 1.21 (available at http://darwin.uvigo.es/software/tcs.html) at the default 95% connection limit.
Mentions: The NJ phenograms were supported by the parsimony network analyses that produced one haplotype group from COI sequences (Fig. 3A) and several for the 5′dloop sequences (Fig. 3B). In particular, Fig. 3A shows that H10 is the most common haplotype, shared between Indian and Atlantic Oceans. Mediterranean haplotypes H1, H2, H3, H5, H6, H15 are separated from H10 by two mutational steps (G-426-A and C-285-T) that represent their nucleotide diagnostics (ND) [22]. Another group of Mediterranean haplotypes (H4, H7, H8, H9) is connected with the Atlantic haplotype H12 and with the H10, that appears as most common haplotype.

Bottom Line: This information was successfully applied to the discrimination of unknown samples from the market, detecting in some cases mislabeled seafood products.Similar results were obtained with 5'dloop.Our preliminary data in swordfish Xiphias gladius confirm that Cytochrome Oxidase I can be proposed as an efficient species-specific marker that has also the potential to assign geographical provenance.

View Article: PubMed Central - PubMed

Affiliation: Section of Biochemistry and Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, National Institute of Biomembranes and Biosystems, Section of Catania, Catania, Italy.

ABSTRACT

Background: The swordfish (Xiphias gladius) is a cosmopolitan large pelagic fish inhabiting tempered and tropical waters and it is a target species for fisheries all around the world. The present study investigated the ability of COI barcoding to reliably identify swordfish and particularly specific stocks of this commercially important species.

Methodology: We applied the classical DNA barcoding technology, upon a 682 bp segment of COI, and compared swordfish sequences from different geographical sources (Atlantic, Indian Oceans and Mediterranean Sea). The sequences of the 5' hyper-variable fragment of the control region (5'dloop), were also used to validate the efficacy of COI as a stock-specific marker.

Case report: This information was successfully applied to the discrimination of unknown samples from the market, detecting in some cases mislabeled seafood products.

Conclusions: The NJ distance-based phenogram (K2P model) obtained with COI sequences allowed us to correlate the swordfish haplotypes to the different geographical stocks. Similar results were obtained with 5'dloop. Our preliminary data in swordfish Xiphias gladius confirm that Cytochrome Oxidase I can be proposed as an efficient species-specific marker that has also the potential to assign geographical provenance. This information might speed the samples analysis in commercial application of barcoding.

Show MeSH