Identification of Edible Fish Species of Pakistan Through DNA Barcoding

Muhammad Zubair Ghouri,Sultan Habibullah Khan,Muhammad Asif Javed,Abdullah Bin Umar,Muhammad Ismail,Mehr-Un-Nisa Mehr-Un-Nisa,Aftab Ahmad,Zulqurnain Khan,Nayla Munawar,Shazia Amin,Syed Ovais Aftab

doi:10.3389/fmars.2020.554183

Abstract

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 (Cyto b) gene. Cyto 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 using the Basic Local Alignment Search Tool. 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.

Highlights

Fish are the most abundant vertebrate group on the earth, consisting of 50% of the vertebrate species
Eleven freshwater fish species belonging to six families and five orders, and six marine fish species belonging to five families and one order were collected (Table 1)
The information generated through this sequence was used to trace the phylogeny of freshwater and marine fish species

Summary

Introduction

Fish are the most abundant vertebrate group on the earth, consisting of 50% of the vertebrate species. Fish consumption is often a staple of the human diet with high digestibility and good taste. Fisheries play an essential role in generating income for many communities (Rafique, 2007; Rafique and Khan, 2012). 33,000 fish species have been identified throughout the world (Di Pinto et al, 2015). In Pakistan, 531 species of fish have been identified, among which. DNA Barcoding of Fish are freshwater and the remaining 298 are marine fish species. According to studies conducted by Rafique (2007) and Rafique and Khan (2012), 78 of the 233 freshwater fish in Pakistan are economically important species

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