Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud
Abstract
1. Introduction
2. Materials and Methods
2.1. mtDNA Genome Data and Sample Collection
2.2. Genomic DNA Extraction
2.3. mtDNA Comparative Analysis
2.4. NAD2 Primer Design and Specificity Test
2.5. End-Point and Real-Time PCR
3. Results
3.1. Sparidae mtDNA Comparative Analysis
3.2. NAD2 Amplification and Analysis
3.3. Real-Time PCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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No | Sparid Species | Ac. Number | FAO Fishing Areas | References |
---|---|---|---|---|
1 | A. latus | NC_010977 | FAO 71 | [26] |
2 | A. schlegelii | JQ_746035 | FAO 71 | [27] |
3 | D. angolensis | NC_044097 | FAO 47 | [22] |
4 | D. dentex | MG_727892 | FAO 37 | [19] |
5 | D. gibbosus | MG_653593 | FAO 37 | [21] |
6 | D. tumifrons | NC_029479 | FAO 71 | [28] |
7 | D. cervinus | NC_064339 | FAO 37 | [25] |
8 | D. hypselosomus | NC_049151 | FAO 61 | [29] |
9 | D. puntazzo | MT319027 | FAO 37 | [23] |
10 | D. sargus | NC_057561 | FAO 37 | [24] |
11 | P. acarne | MG_736083 | FAO 37 | [20] |
12 | P. bogaraveo | NC_009502 | FAO 27 | [30] |
13 | P. erythrinus | MG_653592 | FAO 37 | [18] |
14 | P. auriga | AB_124801 | FAO 37 | [31] |
15 | P. caeruleostictus | MN319701 | FAO 34 | [32] |
16 | P. major | NC_003196 | Andalusia (Spain) fish market | [33] |
17 | P. edita | EF_107158 | FAO 71 | [26] |
18 | R. sarba | KM_272585 | Guangdong (China) | [34] |
19 | S. aurata | LK_022698 | Jaffa (Israel) fish market | [35] |
Sample Abbreviation | GSA | Latitude | Longitude |
---|---|---|---|
Dg1 | 22—Aegean Sea | 37.600.221 | 24.800.000 |
Dg2 | 22—Aegean Sea | 38.167.163 | 25.594.178 |
Dg3 | 6—Northern Spain | 41.865.047 | 3.746.190 |
Dg4 | 4—Algeria | 37.352.717 | 1.778.274 |
Dg5 | 17—Northern Adriatic Sea | 45.110.439 | 12.900.912 |
Dg6 | 10—Southern and Central Tyrrhenian Sea | 39.403.227 | 13.096.640 |
Dg7 | 18—Southern Adriatic Sea | 40.988.637 | 18.420.498 |
Dg8 | 19—Western Ionian Sea | 37.115.696 | 16.486.263 |
Dg9 | 9—Ligurian and North Tyrrhenian Sea | 42.083.042 | 10.191.733 |
Dg10 | 26—Southern Levant Sea | 31.097.963 | 28.197.500 |
No | Scientific Name | Family | Common Name | Abbreviation | Category |
---|---|---|---|---|---|
1 | Arnoglossus laterna | Bothidae | Mediterranean scaldfish | Al | Commercially important Mediterranean fish species |
2 | Aulopus filamentosus | Aulopidae | Royal flagfin | Af | Commercially important Mediterranean fish species |
3 | Boops boops | Sparidae | Bogue | Bb | Commercially important Mediterranean fish species |
4 | Cepola macrophthalma | Cepolidae | Red bandfish | Cm | Commercially important Mediterranean fish species |
5 | Cheimerius nufar | Sparidae | Santer seabream | Cn | Commercially important Mediterranean fish species |
6 | Chelidonichthys lucerna | Triglidae | Tub gurnard | Cl | Commercially important Mediterranean fish species |
7 | Coris julis | Labridae | Rainbow wrasse | Cj | Commercially important Mediterranean fish species |
8 | Dentex angolensis | Sparidae | Angolan dentex | Dn | Used for substitution |
9 | Dentex dentex | Sparidae | Common dentex | Dd | Used for substitution and phylogenetically related |
10 | Dentex tumifrons | Sparidae | Yellowback seabream | Dt | Used for substitution |
11 | Diplodus annularis | Sparidae | Annular seabream | Da | Commercially important Mediterranean fish species |
12 | Diplodus sargus | Sparidae | White seabream | Ds | Commercially important Mediterranean fish species |
13 | Lithognathus mormyrus | Sparidae | Sand steenbras | Lm | Commercially important Mediterranean fish species |
14 | Lophius piscatorius | Lophiidae | Angler (=Monk) | Lp | Commercially important Mediterranean fish species |
15 | Mullus barbatus | Mullidae | Red mullet | Mb | Commercially important Mediterranean fish species |
16 | Pagellus acarne | Sparidae | Axillary seabream | Pa | Commercially important Mediterranean fish species |
17 | Pagellus erythrinus | Sparidae | Common pandora | Pe | Phylogenetically related |
18 | Pleuronectes platessa | Pleuronectidae | European plaice | Pp | Commercially important Mediterranean fish species |
19 | Sebastes capensis | Sebastidae | Cape redfish | Sc | Commercially important Mediterranean fish species |
20 | Scophthalmus maximus | Scophthalmidae | Turbot | Sm | Commercially important Mediterranean fish species |
21 | Solea solea | Soleidae | Common sole | Ss | Commercially important Mediterranean fish species |
22 | Spondyliosoma cantharus | Sparidae | Black seabream | Spc | Commercially important Mediterranean fish species |
23 | Thunnus thynnus | Scombridae | Atlantic bluefin tuna | Tth | Commercially important Mediterranean fish species |
24 | Thunnus albacares | Scombridae | Yellowfin tuna | Ta | Commercially important Mediterranean fish species |
25 | Thunnus obesus | Scombridae | Bigeye tuna | To | Commercially important Mediterranean fish species |
26 | Trachurus trachurus | Carangidae | Atlantic horse mackerel | Tt | Commercially important Mediterranean fish species |
27 | Trisopterus minutus | Gadidae | Poor cod | Tm | Commercially important Mediterranean fish species |
28 | Xyrichtys novacula | Labridae | Pearly razorfish | Xn | Commercially important Mediterranean fish species |
Name | Sequence (5′–3′) | Tm °C | CG% | nt | A | T | C | G |
---|---|---|---|---|---|---|---|---|
1_F_Gib | gcttcttctagccctaggaattacatcaacc | 70.2 | 45.2 | 31 | 8.0 | 9.0 | 10.0 | 4.0 |
1_R_Gib | ctttgatatgaagccggtgagtgggggc | 78.1 | 57.1 | 28 | 5.0 | 7.0 | 4.0 | 12.0 |
2_F_Gib | gcttcttctagccctaggaattac | 61.8 | 45.8 | 24 | 5.0 | 8.0 | 7.0 | 4.0 |
2_R_Gib | ctttgatatgaagccggtgagtg | 66.8 | 47.8 | 23 | 5.0 | 7.0 | 3.0 | 8.0 |
Sequence Variability (Variable Sites/Total Sites) | ||||
---|---|---|---|---|
Genes | Nucleotide | Amino Acid | ||
NAD1 | 389/975 | 40% | 41/325 | 13% |
NAD2 | 530/1047 | 50% | 122/340 | 35% |
COI | 500/1566 | 32% | 33/521 | 6% |
COII | 223/691 | 32% | 22/230 | 10% |
COIII | 258/786 | 33% | 31/262 | 12% |
ATP8 | 72/165 | 42% | 18/55 | 32% |
ATP6 | 308/684 | 53% | 57/228 | 38% |
NAD3 | 136/351 | 39% | 16/117 | 14% |
NAD4L | 116/297 | 39% | 14/99 | 14% |
NAD4 | 610/1386 | 43% | 94/462 | 20% |
NAD5 | 756/1839 | 41% | 127/613 | 21% |
NAD6 | 234/522 | 45% | 48/174 | 6% |
CYTB | 406/1141 | 36% | 34/381 | 9% |
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Venuti, I.; Ceruso, M.; Muscariello, T.; Ambrosio, R.L.; Di Pinto, A.; Pepe, T. Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud. Foods 2023, 12, 3441. https://doi.org/10.3390/foods12183441
Venuti I, Ceruso M, Muscariello T, Ambrosio RL, Di Pinto A, Pepe T. Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud. Foods. 2023; 12(18):3441. https://doi.org/10.3390/foods12183441
Chicago/Turabian StyleVenuti, Iolanda, Marina Ceruso, Tiziana Muscariello, Rosa Luisa Ambrosio, Angela Di Pinto, and Tiziana Pepe. 2023. "Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud" Foods 12, no. 18: 3441. https://doi.org/10.3390/foods12183441
APA StyleVenuti, I., Ceruso, M., Muscariello, T., Ambrosio, R. L., Di Pinto, A., & Pepe, T. (2023). Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud. Foods, 12(18), 3441. https://doi.org/10.3390/foods12183441