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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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Neighbour-Joining distance-based phenograms of (a) swordfish COI barcode and (b) 5′dloop haplotypes from Mediterranean Sea, Atlantic and Indian Oceans identified in this study.Bootstrap values greater than 50 are shown (1000 replicates).
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pone-0025516-g002: Neighbour-Joining distance-based phenograms of (a) swordfish COI barcode and (b) 5′dloop haplotypes from Mediterranean Sea, Atlantic and Indian Oceans identified in this study.Bootstrap values greater than 50 are shown (1000 replicates).

Mentions: The unrooted neighbor-joining phenogram in Figure 2a clearly shows the relationships between all COI haplotypes. In particular, there are two main clusters, one of which includes only haplotypes Mediterranean. In the second cluster there are more different haplotypes. A second node separates four Mediterranean haplotypes (H4, H7, H8, H9) from the Atlantic ones (H12, H13, H14) and within this second cluster there are Atlantic haplotypes mixed with Indian ones. The NJ phenogram (Figure 2b) inferred from 5′dloop haplotypes revealed awell-supported cluster(99%) exclusively containing Mediterranean haplotypes, while other Mediterranean haplotypes are arranged on the other side of the tree, and are muchcloser tothe Atlantic haplotypes. It is likely that these twoclades correspond to those previously identified by Alvarado Bremer et al. [11], [3] using both parsimony and neighbour-joining analyses. Moreover, clade II swordfishes are distinguished by a single repeat of the motif TACA at the beginning of the fragment, whereas clade I sworfishes have two or three contiguous repeats of the motif at this position [11]. In agreement with a previous study [21], clade I was subsequently subdivided into a group presenting two TACA repeats and another with three TACA repeats.


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)

Neighbour-Joining distance-based phenograms of (a) swordfish COI barcode and (b) 5′dloop haplotypes from Mediterranean Sea, Atlantic and Indian Oceans identified in this study.Bootstrap values greater than 50 are shown (1000 replicates).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0025516-g002: Neighbour-Joining distance-based phenograms of (a) swordfish COI barcode and (b) 5′dloop haplotypes from Mediterranean Sea, Atlantic and Indian Oceans identified in this study.Bootstrap values greater than 50 are shown (1000 replicates).
Mentions: The unrooted neighbor-joining phenogram in Figure 2a clearly shows the relationships between all COI haplotypes. In particular, there are two main clusters, one of which includes only haplotypes Mediterranean. In the second cluster there are more different haplotypes. A second node separates four Mediterranean haplotypes (H4, H7, H8, H9) from the Atlantic ones (H12, H13, H14) and within this second cluster there are Atlantic haplotypes mixed with Indian ones. The NJ phenogram (Figure 2b) inferred from 5′dloop haplotypes revealed awell-supported cluster(99%) exclusively containing Mediterranean haplotypes, while other Mediterranean haplotypes are arranged on the other side of the tree, and are muchcloser tothe Atlantic haplotypes. It is likely that these twoclades correspond to those previously identified by Alvarado Bremer et al. [11], [3] using both parsimony and neighbour-joining analyses. Moreover, clade II swordfishes are distinguished by a single repeat of the motif TACA at the beginning of the fragment, whereas clade I sworfishes have two or three contiguous repeats of the motif at this position [11]. In agreement with a previous study [21], clade I was subsequently subdivided into a group presenting two TACA repeats and another with three TACA repeats.

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