Identification of Edible Fish Species of Pakistan Through DNA Barcoding

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 (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.

Saint Peter and Saint Paul Archipelago barcoded: fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

“…The differentiation between species through individual COI barcodes validates the e ciency of COI barcodes for identifying marine sh species. Among the sequences, the AT content (56.30%) was higher than the GC content (43.70%), which is congruent with the constructed SPSPA sh database (AT content: 55.70%) and other COI barcoding of marine sh studies (Ward et al 2005;Steinke et al 2009;Mecklenburg et al 2010;Zhang & Hanner 2011;WS et al 2011;Costa et al 2012;Ribeiro et al 2012;Knebelsberger et al 2014;Bingpeng et al 2018;Limmon et al 2020;Ghouri et al 2020;Ahmed et al 2021). Also, the constructed Neighbor-Joining tree clustered with coherency closely related species under the same nodes, while dissimilar species were clustered under separate nodes.…”

“…The mitochondrial COI gene has been barcoding sh species with high e ciency (Ward 2012;Ward et al 2009). The marine ichthyofauna was successfully characterized in Australia (Ward et al 2005), Antarctic (Rock et al 2008;Mabragaña et al 2016), Canada (Steinke et al 2009), the Arctic (Mecklenburg et al 2010), Japan (Zhang & Hanner 2011), India (WS et al 2011, Portugal (Costa et al 2012), Brazil (Ribeiro et al 2012), Germany (Knebelsberger et al 2014), Taiwan (Bingpeng et al 2018), Indonesia (Limmon et al 2020), Pakistan (Ghouri et al 2020), and Bangladesh (Ahmed et al 2021).…”

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

“…The mitochondrial COI gene has been barcoding fish species with high efficiency ( Ward et al, 2009 ; Ward, 2012 ). The marine ichthyofauna was successfully characterized in Australia ( Ward et al , 2005 ), the Antarctic ( Rock et al, 2008 ; Mabragaña et al, 2016 ), Canada ( Steinke et al, 2009 ), the Arctic ( Mecklenburg et al, 2010 ), Japan ( Zhang and Hanner, 2011 ), India ( Lakra et al, 2011 ), Portugal ( Costa et al, 2012 ), Brazil ( Ribeiro et al, 2012 ), Germany ( Knebelsberger et al , 2014 ), Taiwan ( Bingpeng et al, 2018 ), Indonesia ( Limmon et al, 2020 ), Pakistan ( Ghouri et al. , 2020 ), and Bangladesh ( Ahmed et al, 2021 ).…”

The Application of DNA Barcoding in Crustacean Larvae Identification from the Zhongsha Islands, South China Sea

“…In the decades since a DNA barcoding system for specimen identifications was established, numerous studies have proven that this technique is effective for identifying species (Hajibabaei et al, 2006;Ward et al, 2009;Radulovici et al, 2010). DNA barcoding has now been successfully applied in insects (Janzen et al, 2005;Smith et al, 2005), crustaceans (Costa et al, 2007;Bilgin et al, 2014;Bucklin et al, 2022), fish (Ward et al, 2005;Hubert et al, 2008;Ghouri et al, 2020;Guimarães-Costa et al, 2020;Xu et al, 2021), birds (Hebert et al, 2004), and mammals (Lorenz et al, 2005;Clare et al, 2007). These achievements have benefited from the establishment of the Barcode of Life Data Systems (BOLDSystems), which is a global public standard dataset platform with general technical rules and identification systems for animal taxonomy.…”