Table 1SM The table report the DNA extraction method (Commercial kit and Classical procedure) used in article dealing with fish species identification. The procedure market
with * did not use enzymatic digestion with proteinase K.
Article
Samples
Identifying Canadian Freshwater Fishes through DNA Barcodes
Hubert, et al. (2008). Plos One 3(6): e2490.
Fresh
Method
Commercial kit
Classical procedure
Reference/ Company
MACHEREY-NAGEL GmbH & Co. KG,
NucleoSpin96 kit
D-52313 Düren, Germany
Authentication of Anglerfish Species (Lophius spp) by Means of
Polymerase
Chain
Reaction-Restriction
Fragment
Length
Polymorphism (PCR-RFLP) and Forensically Informative
Nucleotide Sequencing (FINS) Methodologies.
Rogers, et al. (1988). Extraction of DNA from
Fresh/processed
Phenol-chloroform
plant tissues. Plant Molecular Biology Manual.
protocol *
S. Gelvin, R. Schilperoort and D. Verma,
Espineira, et al. (2008). Journal of Agricultural and Food
Springer Netherlands: 73-83.
Chemistry 56 (22): 10594-10599.
DNA barcoding detects market substitution in North American
seafood. Wong & Hanner (2008). Food Research International
41(8): 828-837
Detection
of
Fresh/frying/
precooked
Glass Fiber protocol
utomation-friendly
protocol
for
recovering
high-quality DNA. Molecular Ecology Notes
6(4): 998-1002.
Mislabeling
in
Hake
Seafood
Employing
mtSNPs-Based Methodology with Identification of Eleven Hake
Species of the Genus Merluccius. Machado-Schiaffino, et al.
(2008). Journal of Agricultural and Food Chemistry 56 (13):
5091-5095.
Ivanova, et al. (2006). An inexpensive,
Estoup, et al. (1996). Rapid one-tube DNA
Fresh/frozen/
precooked
extraction for reliable PCR detection of fish
Chelex resin protocol
polymorphic
markers
and
transgenes."
Molecular Marine Biology and Biotechnology
5(4): 295-298.
DNA barcoding for the identification of smoked fish products
Smith, et al. (2008). Journal of Fish Biology 72(2): 464-471.
Phenol–chloroform–eth
Smoked
anol protocol
Taggart, et al. (1992). A simplified protocol
for routine total DNA isolation from salmonid
fishes. Journal of Fish Biology 40(6): 963-965.
MACHEREY-NAGEL GmbH & Co. KG.,
Development of a method for the identification of scombroid and
common substitute species in seafood products by FINS
Espineira, et al. (2009). Food Chemistry 117(4): 698-704.
D-52313 Düren, Germany.
Fresh/frozen/
processed
NucleoSpin Tissue kit
Chloroform-isoamyl
Rogers, et al. (1985). Extraction of DNA from
protocol*
milligram amounts of fresh, herbarium and
mummified plant tissues. Plant Molecular
Biology 5(2): 69-76.
®
PCR-based methodology for the authentication of grouper
(Epinephelus marginatus) in commercial fish fillets.
Wizard DNA
Fresh/processed
Promega Corporation, 2800 Madison, WI
Clean-Up System
53711 USA
Asensio, et al. (2009). Food Control 20(7): 618-622.
The Real maccoyii: Identifying Tuna Sushi with DNA Barcodes
– Contrasting Characteristic Attributes and Genetic Distances
Sushi (fresh)
Lowenstein, et al. (2009). Plos One 4(11): e7866
QIAGEN GmbH, 40724 Hilden, Germany
Tissue Kit
Vinas, et al. (2004). Inter-oceanic genetic
A Validated Methodology for Genetic Identification of Tuna
Species (Genus Thunnus) Vinas, et al. (2009). Plos One
DNeasy Blood &
Fresh
4(10):e7606
Phenol-chloroform-isoa
myl protocol
differentiation
among
albacore
(Thunnus
alalunga) populations. Marine Biology 145(2):
225-232.
Walsh, et al. (1991). Chelex-100 as a medium
for simple extraction of DNA for PCR-based
Identification of shark and ray fins using DNA barcoding
Holmes, et al. (2009). Fisheries Research 95(2-3): 280-288.
Fresh/dried
Chelex resin protocol
typing from forensic material. Biotechniques
Glass Fiber protocol
10(4): 506-513.
Ivanova, et al. (2006). An inexpensive,
automation-friendly protocol for recovering
high-quality DNA. Molecular Ecology Notes
6(4): 998-1002.
The
application of PCR–RFLP
identification
used
in
sea
and
FINS for
cucumbers
species
(Aspidochirotida:
Stichopodidae) products from the market
Fresh/dried
TIANamp Marine
Tiangen Biotech Co. Ltd., Beijing, China
Animals DNA Kit
Wen, et al. (2010). Food Control 21(4): 403-407.
Identification
of
European
Hake
Species
(Merluccius
merluccius) Using Real-Time PCR Sanchez, et al. (2009).
Journal of Agricultural and Food Chemistry 57(9): 3397-3403.
Fresh/ canned/
refrigerated/
Wizard® DNA
precooked/batter
Clean-Up System
Promega Corporation
2800 Madison, WI 53711 USA
ed
Estoup, et al. (1996). "Rapid one-tube DNA
DNA barcoding for conservation and management of Amazonian
commercial fish. Ardura, et al. (2010). Biological Conservation
extraction for reliable PCR detection of fish
Fresh/processed
Chelex resin protocol
143(6): 1438-1443.
polymorphic
markers
and
transgenes."
Molecular Marine Biology and Biotechnology
5(4): 295-298.
A multiplex-PCR assay for the authentication of mackerels of the
genus Scomber in processed fish products. Catanese, et al.
Fresh/canned
MP Biomedicals LLC; QBiogene Division
FastDNA kit*
29525 Fountain Parkway, Solon, OH 44139
(2010). Food Chemistry 122(1): 319-326.
Species identification in anchovy pastes from the market by
PCR-RFLP technique. Rea, et al. (2009). Food Control 20(5):
515-520.
Fresh/processed
Phenol–chloroform
samples
protocol
Sambrook, et al. (1987). Molecular Cloning: A
Laboratory
Manual,
Cold
Spring
Harbor
Laboratory Press. Woodbury, NY, USA
Bio-Rad Laboratories, Inc., 2000 A. Nobel Dr.
Molecular barcoding reveals mislabelling of commercial fish
products in Italy Filonzi, et al. (2010). Food Research
Fresh/processed
International 43(5): 1383-1388.
Aquapure Genomic
DNA
kit
Phenol–chloroform
protocol
Hercules,CA 94547 USA
Moore, et al. (1999). Manipulation of DNA.”
Current protocols in molecular biology, John
Wiley & Sons Inc., New York (1999), 211–223
Application of a PCR-RFLP Method to Identify Salmon Species
Canned/smoked/
DNeasy Blood &
QIAGEN GmbH, 40724 Hilden, Germany
in U.S. Commercial Products Rasmussen, et al. (2010). Journal
jerky/fresh
Tissue Kit
of Aquatic Food Product Technology 19(1): 3-15.
Misleading the masses: detection of mislabelled and substituted
frozen fish products in South Africa Von der Heyden, et al.
Fresh
(2010). Ices Journal of Marine Science 67(1): 176-185.
Authentication of swordfish (Xiphias gladius) by RT–PCR and
FINS methodologies Herrero, et al. (2011).
European Food Research and Technology 233(2): 195-202.
DNeasy Blood &
QIAGEN GmbH, 40724 Hilden, Germany
Tissue Kit
Rogers, et al. (1988). Extraction of DNA from
Fresh/frozen/
Phenol-chloroform
smoked
protocol *
FINS methodology to identification of sardines and related
plant tissues. Plant Molecular Biology Manual.
S. Gelvin, R. Schilperoort and D. Verma,
Springer Netherlands: 73-83.
Rogers, et al. (1988). Extraction of DNA from
species in canned products and detection of mixture by means of
Fresh/processed
Phenol-chloroform
plant tissues. Plant Molecular Biology Manual.
SNP analysis systems. Lago, et al. (2011). European Food
samples
protocol *
S. Gelvin, R. Schilperoort and D. Verma,
Research and Technology 232(6): 1077-1086.
Springer Netherlands: 73-83.
Molecular identification of the black tiger shrimp (Penaeus
monodon), the white leg shrimp (Litopenaeus vannamei) and the
Indian white shrimp (Fenneropenaeus indicus) by PCR targeted
Fresh samples
to the 16S rRNA mtDNA Pascoal, et al. (2011). Food Chemistry
DNeasy Blood &
QIAGEN GmbH, 40724 Hilden, Germany
Tissue Kit
125(4): 1457-1461.
Duplex real-time PCR for authentication of anglerfish species
Herrero, et al. (2011). European Food Research and
Proteinase
Fresh/precooked
Technology 233(5): 817-823.
K-phenol-chloroform
protocol
Rogers, et al. (1988). Extraction of DNA from
plant tissues. Plant Molecular Biology Manual.
S. Gelvin, R. Schilperoort and D. Verma,
Springer Netherlands: 73-83.
Aranishi. (2005). "Rapid PCR-RFLP method
Identification of fish species by 5S rRNA gene amplification
Tognoli, et al. (2011). Food Chemistry 129(4): 1860-1864.
Fresh
Phenol-chloroform-isoa
myl- alcohol protocol
for discrimination of imported and domestic
mackerel."
Marine
Biotechnology
7(6):
571-575.
DNA barcoding unveils a high rate of mislabeling in a
commercial freshwater catfish from Brazil.
Fresh
Phenol-chloroform
protocol
Sambrook, et al. (1989). Molecular Cloning: A
Laboratory
Manual,
Cold
Spring
Harbor
Carvalho, et al. (2011). Mitochondrial DNA 22: 97-105.
Laboratory Press. Woodbury, NY, USA
High Level of Mislabeling in Spanish and Greek Hake Markets
Moran, et al. (2006). "Identification of highly
Suggests the Fraudulent Introduction of African Species
Garcia-Vazquez, et al. (2011). Journal of Agricultural and
Fresh
Chelex resin protocol
Food Chemistry 59(2): 475-480.
prized commercial fish using a PCR-based
methodology." Biochemistry and Molecular
Biology Education 34(2): 121-124.
Rehbein. (2005). "Identification of the fish
Identification of barramundi (Lates calcarifer) and tilapia
(Oreochromis spp.) fillets by DNA- and protein-analytical
methods.
Schiefenhoevel,
et
al.
(2011).
Verbraucherschutz Und Lebensmittelsicherheit
Journal
Fur
species of raw or cold-smoked salmon and
Chloroform-
Fresh
isopropanol
protocol
6(2): 203-214.
salmon caviar by single-strand conformation
polymorphism (SSCP) analysis." European
Food Research and Technology 220(5-6):
625-632.
DNA Barcoding of Catfish: Species Authentication and
Phylogenetic Assessment. Wong, et al. (2011). Plos One
Fin clip (fresh)
6(3):e17812
DNA barcoding reveals a high incidence of fi sh species
misrepresentation and substitution on the South African market
Cawthorn, et al. (2012). Food Research International 46(1):
Fresh/frozen/pro
cessed
Gentra Puregene Tissue
QIAGEN GmbH, 40724 Hilden, Germany
Kit
SureFood® PREP
R-Biopharm AG, 64297 Darmstadt, Germany
Allergen Kit
30-40.
Chemical characterisation, biogenic amines contents, and
identification of fish species in cod and escolar steaks, and salted
escolar roe products. Hwang, et al. (2012). Food Control 25(1):
Fresh/salted
Chemagic DNA Tissue
PerkinElmer Chemagen Technologie GmbH
10 Kit *
52499 Baesweiler, Germany
415-420.
A unique specification method for processed unicorn filefish
products using a DNA barcode marker. Yang, et al. (2012).
Food Control 25(1): 292-302.
Authentication of commercialized crab-meat in Chile using DNA
Barcoding.
Haye, et al. (2012). Food Control 25(1): 239-244.
Canned/dried/
MasterPure™ DNA
fried
Purification Kit
Fresh/canned
Epicentre Biotechnologies, Madison, WI, 53719
USA
Phenol-Chloroform
method
Sambrook, et al. (1989). Molecular Cloning: A
Laboratory
Manual,
Cold
Spring
Laboratory Press. Woodbury, NY, USA
Harbor
Estoup, et al. (1996). "Rapid one-tube DNA
Inaccurate labelling detected at landings and markets: The case
of European megrims. Crego-Prieto, et al. (2012). Fisheries
extraction for reliable PCR detection of fish
Fresh samples
Chelex resin protocol
Research 129: 106-109.
polymorphic
markers
and
transgenes."
Molecular Marine Biology and Biotechnology
5(4): 295-298.
Identification of 11 sea cucumber species by species-specific
PCR method. Wen, et al. (2013). Food Control 29(1): 287-287.
DNA Barcoding as a Reliable Method for the Authentication of
Commercial Seafood Products Nicole, et al. (2012). Food
Technology and Biotechnology 50(4): 387-398.
TIANamp
Fresh/fresh/dried
Fresh/frozen/sm
oked/dried
Canned/fresh/
fish in commercial aquaculture fish meals
smoked/salty/
dried
GenElute Mammalian
Sigma-Aldrich, LLC., St. Louis, Missouri
Genomic DNA
63103 United States
Miniprep Kit
QIAamp® DNA Mini
QIAGEN GmbH, 40724 Hilden, Germany
Kit
Rogers, et al. (1988). Extraction of DNA from
Authentication of the most important species of freshwater eels
by means of FINS. Lago, et al. (2012). European Food Research
Tiangen Biotech Co. Ltd., Beijing, China
Kit
Forensic DNA analysis reveals use of high trophic level marine
Ardura, et al. (2012). Fisheries Research 115: 115-120.
Marine Animals DNA
Frozen
and Technology 234(4): 689-694.
Phenol and chloroform
plant tissues. In: Plant Molecular Biology
protocol *
Manual. S. Gelvin, R. Schilperoort and D.
Verma, Springer Netherlands: 73-83.
Development of real-time PCR assays for the detection of
Meyer, et al. (1994). Detection of pork in
Atlantic cod (Gadus morhua), Atlantic salmon (Salmo salar) and
Fresh/cooked/
European plaice (Pleuronectes platessa) in complex food
autoclave
Chloroform protocol
samples. Hird, et al. (2012). Eu. Food Res.Tech234(1): 127-136.
Kang, et al. (1998). A rapid DNA extraction
Dried/canned
137-142.
Detection and quantification of tissue of origin in salmon and
veal products using methylation sensitive AFLPs. Rodriguez
reaction. Journal of AOAC International 77(3):
617-622.
Application of FINS and multiplex PCR for detecting genuine
abalone products. Chan, et al. (2012). Food Control 23(1):
heated meat products by the polymerase chain
Phenol-chloroform-isoa
method for RFLP and PCR analysis from a
myl protocol*
single dry seed. Plant Molecular Biology
Reporter 16(1): 90-90.
Fresh
NucleoSpin® Tissue
Kit
MACHEREY-NAGEL GmbH & Co. KG,
D-52313 Düren, Germany
Lopez, et al. (2012). Food Chemistry 131(4): 1493-1498.
Identification of tuna species by a real-time polymerase chain
reaction technique Chuang, et al. (2012). Food Chemistry
133(3): 1055-1061.
Fresh/canned
DNeasy Blood &
samples
Tissue Kit
Molecular identification of fish species from surimi-based
products labeled as Alaskan Pollock. Keskin, et al. (2012).
Surimi
Journal of Applied Ichthyology 28(5): 811-814.
DNA barcoding commercially important fish species of Turkey
Keskin, et al. (2013). Molecular Ecology Resources 13(5):
Fresh muscle
788-797.
QIAGEN GmbH, 40724 Hilden, Germany
DNeasy Blood &
QIAGEN GmbH, 40724 Hilden, Germany
Tissue Kit
DNeasy Blood &
QIAGEN GmbH, 40724 Hilden, Germany
Tissue Kit
Detection of mislabeled commercial fishery by-products in the
Philippines using DNA barcodes and its implications to food
traceability and safety
Santos, et al. (2010). A pilot study on the
Fresh/frozen
Chloroform protocol
Maralit, et al. (2013). Food Control 33(1): 119-125.
Ensuring seafood identity: Grouper identification by real-time
nucleic acid sequence-based amplification (RT-NASBA)
Ulrich, et al. (2013). Food Control 31(2): 337-344.
Rapid species identification of fresh and processed scallops by
multiplex PCR Marin, et al. (2013). Food Control 32(2):
472-476.
genetic
variation
(Euthynnus
of
affinis)
Eastern
in
little
Southeast
tuna
Asia.
Philippine Journal of Science, 139 (1): 43–50
Fresh/frozen/
ethanol
preserved
DNeasy Blood &
QIAGEN GmbH, 40724 Hilden, Germany
Tissue Kit
Sokolov. (2000). "An improved method for
Fresh/canned/
Phenol-chloroform
boiled
protocol
DNA isolation from mucopolysaccharide-rich
molluscan tissues."
Journal of Molluscan
Studies 66: 573-575.
A novel minisequencing test for species identification of salted
and dried products derived from species belonging to
Fresh/salted/
DNeasy Blood &
Gadiformes Dalmasso, et al. (2013). Food Control 34(2):
dried samples
Tissue Kit
QIAGEN GmbH, 40724 Hilden, Germany
296-299.
Commercialization of a critically endangered species (largetooth
sawfish, Pristis perotteti) in fish markets of northern Brazil:
Authenticity by DNA analysis Melo Palmeira, et al. (2013).
Fresh/salted
Phenol-chlorophorm
samples
protocol
Sambrook, et al. (2001). Molecular Cloning: A
Laboratory
Manual,
Cold
Spring
Laboratory Press. Woodbury, NY, USA
Harbor
Food Control 34(1): 249-252.
DNA barcoding for detecting market substitution in salted cod
fillets and battered cod chunks Di Pinto, et al. (2013). Food
Salted
Chemistry 141(3): 1757-1762.
DNeasy Blood &
QIAGEN GmbH, 40724 Hilden, Germany
Tissue Kit
Promega Corporation, 2800 Madison, WI
Development of a rapid genetic technique for the identification
53711 USA ;
of clupeid larvae in the Western English Channel and
Estoup, et al. (1996). Rapid one-tube DNA
investigation of mislabeling in processed fish products.
Fresh/processed
Wizard kit for adult fish
Chelex resin protocol
extraction for reliable PCR detection of fish
Brechon, et al. (2013). Ices Journal of Marine Science 70(2):
polymorphic markers and transgenes. Molecular
399-407.
Marine
Biology
and
Biotechnology
5(4):
295-298.
Rehbein. (2005). Identification of the fish
Differentiation of Sparidae species by DNA sequence analysis,
PCR-SSCP and IEF of sarcoplasmic proteins. Schiefenhoevel, et
al. (2013). Food Chemistry 138(1): 154-160.
Frozen/processe
d samples
Chloroformisopropanol
protocol
species of raw or cold-smoked salmon and
salmon caviar by single-strand conformation
polymorphism (SSCP) analysis. European Food
Research and Technology 220(5-6): 625-632.
Table 2SM Level of significance, evaluated using two mixed models with REML estimation of variance, of the effects associated to the factors method (M), species (S), and
interaction between method and species (M*S) (model 1), or method (M), category (C), and interaction between method and category (M*C) (model 2) on yield, A260/A280, and
A260/A230 for fresh and ethanol preserved samples. *** p<0.001; ** p<0.01; * p<0.05; ns=non significant.
Fresh
Ethanol
Yield
A260/A280
A260/A230
Yield
A260/A280
A260/A230
M
***
***
***
***
***
ns
S
***
***
***
***
***
ns
M*S
***
***
***
***
***
ns
M
***
***
***
***
***
ns
C
**
ns
*
ns
ns
ns
M*C
***
*
***
ns
ns
ns