TY - JOUR
T1 - Identification of Edible Fish Species of Pakistan Through DNA Barcoding
AU - Ghouri, Muhammad Zubair
AU - Ismail, Muhammad
AU - Javed, Muhammad Asif
AU - Khan, Sultan Habibullah
AU - Munawar, Nayla
AU - Umar, Abdullah Bin
AU - Mehr-un-Nisa, Abdullah Bin
AU - Aftab, Syed Ovais
AU - Amin, Shazia
AU - Khan, Zulqurnain
AU - Ahmad, Aftab
N1 - Funding Information:
We thank Office of Research, Innovation and Commercialization (ORIC), University of Agriculture, Faisalabad, Pakistan for their help in grant and research work.
Funding Information:
Work in lab of AA has been supported by Higher Education Commission, Islamabad, Pakistan under grant # NRPU-6350.
Publisher Copyright:
© Copyright © 2020 Ghouri, Ismail, Javed, Khan, Munawar, Umar, Nisa, Aftab, Amin, Khan and Ahmad.
PY - 2020/11/4
Y1 - 2020/11/4
N2 - Fish is a fundamentally healthy food, loaded with essential nutrients, high protein content, vitamin D, and omega-three fatty acid. Mislabeling is a common problem in the fish industry that causes an imbalance in prices and fluctuation in the market. DNA barcoding is a potential technique for authentication of mislabeled and misidentified fish species. In this study, 11 freshwater and 6 marine fish species were used for DNA barcoding and further authentication using the mitochondrial cytochrome b (Cyt b) gene. Cyt b was amplified using PCR, producing an average read length of 1,141 bp. The obtained sequences were compared to the National Center for Biotechnology Information database (NCBI) using the Basic Local Alignment Search Tool (BLAST). The average AT content (55.20%) was higher than the average GC content (44.78%) in marine and freshwater fish species. The mean genetic Kimura 2-parameter distances for species, genus, families, and orders were 0.311, 0.308, 0.023, and 0.337, respectively. Phylogenetic tree analysis revealed that most of the freshwater fish species clustered together due to the fact that they were in the same order or family, while the marine fish species clustered distantly. Single nucleotide polymorphism (SNP) analysis of all species in the study revealed distinct features regarding unique sites. All fish species could be identified based on their unique SNP profiles. Based on SNP data, DNA sequence based QR codes were developed for accurate identification of fish species. This is the first study to develop DNA-based QR barcodes for proper authentication of species during the chain of custody using simple technology.
AB - Fish is a fundamentally healthy food, loaded with essential nutrients, high protein content, vitamin D, and omega-three fatty acid. Mislabeling is a common problem in the fish industry that causes an imbalance in prices and fluctuation in the market. DNA barcoding is a potential technique for authentication of mislabeled and misidentified fish species. In this study, 11 freshwater and 6 marine fish species were used for DNA barcoding and further authentication using the mitochondrial cytochrome b (Cyt b) gene. Cyt b was amplified using PCR, producing an average read length of 1,141 bp. The obtained sequences were compared to the National Center for Biotechnology Information database (NCBI) using the Basic Local Alignment Search Tool (BLAST). The average AT content (55.20%) was higher than the average GC content (44.78%) in marine and freshwater fish species. The mean genetic Kimura 2-parameter distances for species, genus, families, and orders were 0.311, 0.308, 0.023, and 0.337, respectively. Phylogenetic tree analysis revealed that most of the freshwater fish species clustered together due to the fact that they were in the same order or family, while the marine fish species clustered distantly. Single nucleotide polymorphism (SNP) analysis of all species in the study revealed distinct features regarding unique sites. All fish species could be identified based on their unique SNP profiles. Based on SNP data, DNA sequence based QR codes were developed for accurate identification of fish species. This is the first study to develop DNA-based QR barcodes for proper authentication of species during the chain of custody using simple technology.
KW - DNA barcoding
KW - QR barcodes
KW - SNPs
KW - fish
KW - freshwater
KW - identification
KW - marine water
KW - mislabeling
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U2 - 10.3389/fmars.2020.554183
DO - 10.3389/fmars.2020.554183
M3 - Article
AN - SCOPUS:85096163308
SN - 2296-7745
VL - 7
JO - Frontiers in Marine Science
JF - Frontiers in Marine Science
M1 - 554183
ER -