Abstract
The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine) for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon) as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43%) in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97) and lower for avian species (0.70). PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.
Highlights
The possibility to identify the species of origin of meat and meat products is an important issue to prevent and detect frauds that derive from the economic incentives to substitute premiumPLOS ONE | DOI:10.1371/journal.pone.0121701 April 29, 2015Identification of Meat Species by Generation SequencingBologna
We evaluated the potential of generation semiconductor based sequencing technology for the identification of meat species by sequencing PCR products obtained from different universal primer pairs that amplify mitochondrial DNA (mtDNA) genes
This is due to intraspecific variability that has been already reported in mtDNA of many species that does not prevent the attribution of the target amplified regions to the correct species [20]
Summary
The possibility to identify the species of origin of meat and meat products is an important issue to prevent and detect frauds that derive from the economic incentives to substitute premiumPLOS ONE | DOI:10.1371/journal.pone.0121701 April 29, 2015Identification of Meat Species by Generation SequencingBologna. The possibility to identify the species of origin of meat and meat products is an important issue to prevent and detect frauds that derive from the economic incentives to substitute premium. The authors confirm that this does not alter their adherence to all PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors, http://www.PLOSone.org/static/ editorial.action#competing. Meat or high added-value products with products of lower quality obtained from cheaper species. Substitutions could be derived by accidental events and labelling errors. All these substitutions can have economic implications but may rise concerns related to food safety and security, lifestyle, religious and ethical aspects and are main objectives in forensics investigations [1]
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