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Food Analytical Methods

, Volume 9, Issue 5, pp 1199–1209 | Cite as

Universal Primers Used for Species Identification of Foodstuff of Animal Origin: Effects of Oligonucleotide Tails on PCR Amplification and Sequencing Performance

  • A. ArmaniEmail author
  • A. Giusti
  • L. Guardone
  • L. Castigliego
  • D. Gianfaldoni
  • A. Guidi
Article

Abstract

M13 universal non-homologous oligonucleotide tails incorporated into universal primers have been shown to improve amplification and sequencing performance. However, a few protocols use these tails in the field of food inspection. In this study, two types of M13 tails (by Steffens and Messing) were selected to assess their benefits using universal cytochrome oxidase subunit I (COI) and 16S ribosomal RNA gene (16SrRNA) primers in standard procedures. The primer characteristics were tested in silico. Then, using 20 DNA samples of edible species (birds, fishes, and mammals), their performance during PCR amplification (band recovery and intensity) and sequencing (sequence recovery, length, and Phred score) was assessed and compared. While 16SrRNA tailed and non-tailed primers performed similarly, differences were found for COI primers. Messing’s tails negatively affected the reaction outputs, while Steffens’ tails significantly improved the band intensity and the length of the final contigs based on the individual bidirectional read sequence. This different performance could be related to a destabilization effect of certain tails on primers with unfavorable mismatches on the annealing region. Even though our results cannot be generalized because the tail performances are strictly dependent on laboratory conditions, they show that appropriate tails can improve the overall throughput of the analysis, supporting food traceability.

Keywords

Universal primers M13 oligonucleotide tails Tailed primers Species identification Amplification Sequencing 

Notes

Acknowledgments

The research was performed with funds granted from the University of Pisa.

Conflict of Interest

Armani Andrea declares that he has no conflict of interest. Giusti Alice declares that she has no conflict of interest. Guardone Lisa declares that she has no conflict of interest. Castigliego Lorenzo declares that he has no conflict of interest. Gianfaldoni Daniela declares that she has no conflict of interest. Guidi Alessandra declares that she has no conflict of interest. This article does not contain any studies with human or animal subjects.

Supplementary material

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Table 1SM (DOCX 32 kb)
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Table 4SM (DOCX 13 kb)

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • A. Armani
    • 1
    Email author
  • A. Giusti
    • 1
  • L. Guardone
    • 1
  • L. Castigliego
    • 1
  • D. Gianfaldoni
    • 1
  • A. Guidi
    • 1
  1. 1.FishLab, Department of Veterinary SciencesUniversity of PisaPisaItaly

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