Table 1SM. Main DNA Barcoding Studies for Fishes Identification with Primers Used

Table 1SM. Main DNA barcoding studies for fishes identification with primers used.

Authors / Studytitle / Primersused and reference1 / Oligonucleotidetailsused / Field of application
Ward et al., 2005 / DNA barcoding Australia’s fish species / Fish F1/ Fish R1 and Fish F2/ Fish R2 / - / Foodinspection
Ivanova et al., 2007 / Universal primer cocktails for fish DNA barcoding / FF2d/FR1d/FR1d_t1;
VF1_t1/VF1d_t1/VF1i_t1/VR1d_t1/VR1i_t1
(Ivanova et al., 2006)
LepF1_t1 and LepRI_t1
(Hebert et al., 2004)
VR1_t1/VF2_t1/FishF2_t1/FishR2_t1
(Ward et al., 2005) / M13F (-21) and M13R (-27)
(Messing, 1983) / Evolutionarystudies
Wong and Hanner, 2008 / DNA barcoding detects market substitution in North American seafood / C_FishF1t1 and
C_FishR1t1
(Ivanova et al., 2007) / M13F (-21) and M13R (-27)
(Messing, 1983) / Foodinspection
Smith et al., 2008 / DNA barcoding for the identification of
smokedfishproducts / Fish F2 and FishR2
(Ward et al., 2005) / - / Foodinspection
Baldwin et al., 2009 / Genetic identification and color descriptions of early life-history stages of
Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae)
with Comments on identification of adult Phaeoptyx / FISH-BCL and FISH-BCH / - / Evolutionarystudies
Rasmussen et al., 2009 / DNA Barcoding of Commercially Important Salmon and Trout
Species(OncorhynchusandSalmo)from North America / C_FishF1t1 and
C_FishR1t1
(Ivanova et al., 2007) / M13F (-21) and M13R (-27)
(Messing, 1983) / Foodinspection
Holmes et al., 2009 / Identification of shark and ray fins using DNA barcoding / C_FishF1t1 and
C_FishR1t1
(Ivanova et al., 2007) / M13F (-21) and M13R (-27)
(Messing, 1983) / Foodinspection
Ardura et al., 2010 / DNA barcoding for conservation and management of Amazonian commercial fish / Fish F1/ Fish R1 and Fish F2/ Fish R2
(Ward et al., 2005) / - / Foodinspection
Barbuto et al., 2010 / DNA barcoding reveals fraudulent substitutions in shark seafood products:
The Italian case of ‘‘palombo” (Mustelus spp.) / Fish R2 and Shark-int
(Ward et al., 2005) / - / Foodinspection
Filonzi et al., 2010 / Molecular barcoding reveals mislabelling of commercial fish products in Italy / COI-ff2d-fish and COI-fr1d-fish
(Ivanova et al., 2007) / - / Foodinspection
Kochzius et al., 2010 / Identifying Fishes through DNA Barcodes and
Microarrays / Fish F1 and FishR1
(Ward et al., 2005) / - / Foodinspection
Carvalho et al., 2011 / DNA barcoding unveils a high rate of mislabeling in a commercial freshwater catfish from Brazil / Fish F1 and FishR1
(Ward et al., 2005) / - / Foodinspection
Handy et al., 2011 / A Single-Laboratory Validated Method for the Generation of DNA Barcodes for the Identification of Fish for Regulatory Compliance / FISH-BCL and FISH-BCH
(Baldwin et al., 2009) / M13F (-29) and M13R
(Steffens, 1993) / Foodinspection
Zhang and Hanner, 2011 / DNA barcoding is a useful tool for the identification of marine fishes from Japan / FishF2_t1, VF2_t1, FishR2_t1, FR1d_t1
(Ivanova et al., 2007) / M13F (-21) and M13R (-27)
(Messing, 1983) / Evolutionarystudies
Cawthorn et al., 2012 / DNA barcoding reveals a high incidence offish species misrepresentation and
substitution on the South African market / C_FishF1t1 and
C_FishR1t1
(Ivanova et al., 2007) / M13F (-21) and M13R (-27)
(Messing, 1983) / Foodinspection
Haye et al., 2012 / Authentication of commercialized crab-meat in Chile using DNA barcoding / LCO1490 and HCO2198
(Folmer et al., 1994) / - / Foodinspection
Huxley-Jones et al., 2012 / Use of DNA barcoding to reveal species composition of convenience seafood / VF1 and VR1d
(Ivanova et al., 2007) / M13F (-21) and M13R (-27)
(Messing, 1983)
Di Pinto et al., 2013 / DNA barcoding for detecting market substitution in salted cod fillets
and batteredcodchunks / FISHCOILBC and FISHCOIHBC (Handy et al. 2011) / - / Foodinspection
Keskin and Atar, 2013 / DNA barcoding commercially important fish
species of Turkey / Fish F2 and FishR2
(Ward et al., 2005) / - / Foodinspection
Maralit et al., 2013 / Detection of mislabeled commercialfishery by-products in the
Philippines using DNA barcodes and its implications to food
traceability and safety / LCO1490 and HCO2198
(Folmer et al., 1994) / - / Foodinspection
Abdullah and Rehbein, 2014 / Authentication of raw and processed tuna from Indonesian
markets using DNA barcoding, nuclear gene and character‑based
approach / Fish F1 and FishR1
(Ward et al., 2005) / M13F (-21) and M13R (-27)
(Messing, 1983) / Foodinspection
Chakraborty, 2014 / An assessment of the DNA barcodes of Indian freshwater fishes / Fish F1 and FishR1
(Ward et al., 2005) / - / Foodinspection
Cutarelli et al., 2014t / Italian market fish species identification and commercial frauds
revealing by DNA sequencing / Fish F2 and FishR2
(Ward et al., 2005) / - / Foodinspection
Galal-Khallaf et al., 2014 / DNA barcoding reveals a high level of mislabeling in Egyptian fish
fillets / Fish F1 and FishR1
Fish F2 and FishR2
(Ward et al., 2005) / - / Foodinspection
Lamendin et al., 2014 / Labelling accuracy in Tasmanian seafood: an investigation using DNA barcoding / Fish F1 and FishR1
(Ward et al., 2005) / - / Foodinspection
Carvalho et al., 2015 / DNA Barcoding identification of commercialized seafood in SouthBrazil: A governmental regulatory forensic program / Fish F1 and FishR1
(Ward et al., 2005) / - / Foodinspection

1When not reported, the primers have been developed by the authors of the study.Rows in grey highlights studies which used oligonucleotides tails.

eferences:

Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. (2005). DNA barcoding Australia's fish species.Philosophical Transactions of the Royal Society B: Biological Sciences,360(1462), 1847-1857

Ivanova, N. V., Zemlak, T. S., Hanner, R. H., & Hebert, P. D. (2007). Universal primer cocktails for fish DNA barcoding.Molecular Ecology Notes,7(4), 544-548

Wong, E. H. K., & Hanner, R. H. (2008). DNA barcoding detects market substitution in North American seafood.Food Research International,41(8), 828-837

Smith, P. J., McVeagh, S. M., & Steinke, D. (2008). DNA barcoding for the identification of smoked fish products.Journal of Fish Biology,72(2), 464-471

Baldwin, C. C., Mounts, J. H., Smith, D. G., & Weigt, L. A. (2009). Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx.Zootaxa,2008, 1-22

Rasmussen, R. S., Morrissey, M. T., & Hebert, P. D. (2009). DNA barcoding of commercially important salmon and trout species (Oncorhynchus and Salmo) from North America.Journal of agricultural and food chemistry,57(18), 8379-8385

Holmes, B. H., Steinke, D., & Ward, R. D. (2009). Identification of shark and ray fins using DNA barcoding.Fisheries Research,95(2), 280-288

Ardura, A., Linde, A. R., Moreira, J. C., & Garcia-Vazquez, E. (2010). DNA barcoding for conservation and management of Amazonian commercial fish.Biological Conservation,143(6), 1438-1443

Barbuto, M., Galimberti, A., Ferri, E., Labra, M., Malandra, R., Galli, P., & Casiraghi, M. (2010). DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo”(Mustelus spp.).Food Research International,43(1), 376-381

Filonzi, L., Chiesa, S., Vaghi, M., & Marzano, F. N. (2010). Molecular barcoding reveals mislabelling of commercial fish products in Italy.Food Research International,43(5), 1383-1388

Kochzius, M., Seidel, C., Antoniou, A., Botla, S. K., Campo, D., Cariani, A., ... Blohm, D. (2010). Identifying fishes through DNA barcodes and microarrays.PLoS One,5(9), e12620

Carvalho, D. C., Neto, D. A., Brasil, B. S., & Oliveira, D. A. (2011). DNA barcoding unveils a high rate of mislabeling in a commercial freshwater catfish from Brazil.Mitochondrial DNA,22(S1), 97-105

Chakraborty, M., & Ghosh, S. K. (2014). An assessment of the DNA barcodes of Indian freshwater fishes.Gene,537(1), 20-28.

Handy, S. M., Deeds, J. R., Ivanova, N. V., Hebert, P. D., Hanner, R. H., Ormos, A., ... & Yancy, H. F. (2011). A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance.Journal of AOAC International,94(1), 201-210

Zhang, J. B., & Hanner, R. (2011). DNA barcoding is a useful tool for the identification of marine fishes from Japan.Biochemical Systematics and Ecology,39(1), 31-42

Cawthorn, D. M., Steinman, H. A., & Witthuhn, R. C. (2012). DNA barcoding reveals a high incidence of fish species misrepresentation and substitution on the South African market.Food Research International,46(1), 30-40.

Haye, P. A., Segovia, N. I., Vera, R., de losÁngelesGallardo, M., & Gallardo-Escárate, C. (2012). Authentication of commercialized crab-meat in Chile using DNA barcoding.Food Control,25(1), 239-244.

Huxley‐Jones, E., Shaw, J. L., Fletcher, C., Parnell, J., & Watts, P. C. (2012). Use of DNA barcoding to reveal species composition of convenience seafood.ConservationBiology,26(2), 367-371

Di Pinto, A., Di Pinto, P., Terio, V., Bozzo, G., Bonerba, E., Ceci, E., & Tantillo, G. (2013). DNA barcoding for detecting market substitution in salted cod fillets and battered cod chunks.Food chemistry,141(3), 1757-1762

Keskİn, E., & Atar, H. H. (2013). DNA barcoding commercially important fish species of Turkey.Molecular ecology resources,13(5), 788-797

Maralit, B. A., Aguila, R. D., Ventolero, M. F. H., Perez, S. K. L., Willette, D. A., & Santos, M. D. (2013). Detection of mislabeled commercial fishery by-products in the Philippines using DNA barcodes and its implications to food traceability and safety.Food Control,33(1), 119-125

Abdullah, A., & Rehbein, H. (2014). Authentication of raw and processed tuna from Indonesian markets using DNA barcoding, nuclear gene and character-based approach.EuropeanFoodResearch and Technology,239(4), 695-706

Cutarelli, A., Amoroso, M. G., De Roma, A., Girardi, S., Galiero, G., Guarino, A., & Corrado, F. (2014). Italian market fish species identification and commercial frauds revealing by DNA sequencing.Food Control,37, 46-50

Galal-Khallaf, A., Ardura, A., Mohammed-Geba, K., Borrell, Y. J., & Garcia-Vazquez, E. (2014). DNA barcoding reveals a high level of mislabeling in Egyptian fish fillets.Food Control,46, 441-445

Lamendin, R., Miller, K., & Ward, R. D. (2015). Labelling accuracy in Tasmanian seafood: An investigation using DNA barcoding.Food Control,47, 436-443

Carvalho, D. C., Palhares, R. M., Drummond, M. G., & Frigo, T. B. (2015). DNA Barcoding identification of commercialized seafood in South Brazil: A governmental regulatory forensic program.Food Control,50, 784-788

FoodAnalyticalMethods

“Universal primers used for species identification of foodstuff of animal origin: effects of oligonucleotide tails on PCR amplification and sequencing performance”

Armani A.*, Giusti A., Guardone L., Castigliego L., Gianfaldoni D., Guidi A.

*FishLab, ( Department of Veterinary Sciences, University of Pisa, VialedellePiagge 2, 56124, Pisa (Italy).

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