Use of the chloroplast gene ycf1 for the genetic differentiation of pine nuts obtained from consumers experiencing dysgeusia

Journal of Agricultural and Food Chemistry

Volumn 59, Issue 20, 2011, Pages 10995-11002

  Handy, Sara M ^a   Parks, Matthew B ^b   Deeds, Jonathan R ^a   Liston, Aaron ^b   De Jager, Lowri S ^a   Luccioli, Stefano ^a   Kwegyir Afful, Ernest ^a   Fardin Kia, Ali R ^a   Begley, Timothy H ^a   Rader, Jeanne I ^a   Diachenko, Gregory W ^a  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^b OREGON STATE UNIVERSITY   (United States)

Author keywords

DNA; dysgeusia; pine mouth; pine nut; Pinus armandii; ycf1

Indexed keywords

DYSGEUSIA; PINE MOUTH; PINE NUT; PINUS ARMANDII; YCF1;

CHLOROPHYLL; FATTY ACIDS; GAS CHROMATOGRAPHY; IONIZATION OF GASES;

GENES;

CHLOROPLAST DNA; VEGETABLE PROTEIN;

ARTICLE; CHEMISTRY; CLASSIFICATION; DYSGEUSIA; GENETICS; HUMAN; NUT; PINE; POLYMERASE CHAIN REACTION;

DNA, CHLOROPLAST; DYSGEUSIA; HUMANS; NUTS; PINUS; PLANT PROTEINS; POLYMERASE CHAIN REACTION;

PINUS ARMANDII;

EID: 80054975953     PISSN: 00218561     EISSN: 15205118     Source Type: Journal    
DOI: 10.1021/jf203215v     Document Type: Article

References (33)

1. Mostin, M. Taste disturbances after pine nut ingestion Eur. J. Emerg. Med. 2001, 8 (1) 76
2. Munk, M. D. Pine Mouth" syndrome: cacogeusia following ingestion of pine nuts (genus: Pinus). An emerging problem? J. Med. Toxicol. 2010, 6 (2) 158-159
3. Kwegyir-Afful, E.; DeJager, L.; Begley, T.; Luccioli, S. Pine mouth syndrome- an emerging food hypersensitivity? Clin. Transl. Allergy 2011, 1 (Suppl. 1) 25
4. Destaillats, F; Cruz-Hernandez, C; Giuffrida, F; Dionisi, F; Mostin, M; Verstegen, G. Identification of the Botanical Origin of Commercial Pine Nuts Responsible for Dysgeusia by Gas-Liquid Chromatography Analysis of Fatty Acid profile J. Toxicol. 2011, 1-7
5. Köbler, H.; Monakhova, Y. B.; Kuballa, T.; Tschiersch, C.; Vancutsem, J.; Thielert, G.; Mohring, A.; Lachenmeier, D. W. Nuclear magnetic resonance spectroscopy and chemometrics to identify pine nuts that cause taste disturbance J. Agric. Food Chem. 2011, 59 (13) 6877-6881
6. Fardin-Kia, A. R.; Handy, S. M.; Rader, J. I. Use of the highly polar SLB-IL111 GC column to determine the fatty acid composition of different species of pine nuts and comparison with "Pine Mouth" associated pine nuts. Unpublished.
7. Saker, M. L.; Welker, M.; Vasconcelos, V. M. Multiplex PCR for the detection of toxigenic cyanobacteria in dietary supplements produced for human consumption Appl. Microbiol. Biotechnol. 2007, 73, 1136-1142 (Pubitemid 44974323)
8. Rasmussen-Hellberg, R. S.; Morrissey, M. T. Advances in DNA-based techniques for the detection of seafood species substitution on the commercial market J. Lab. Autom. 2011, 16 (4) 308-321
9. Focke, F.; Haase, I.; Fischer, M. DNA-based identification of spices: DNA isolation, whole genome amplification, and polymerase chain reaction J. Agric. Food Chem. 2011, 59 (2) 513-520
10. Brzezinski, J. L. Detection of sesame seed DNA in foods using real-time PCR J. Food Prot. 2007, 70 (4) 1033-6 (Pubitemid 46608829)
11. Brezná, B.; Dudásová, H.; Kuchta, T. A novel real-time polymerase chain reaction method for the detection of Brazil nuts in food J. AOAC Int. 2010, 93 (1) 197-201
12. Hebert, P. D. N.; Cywinska, A.; Ball, S. L.; deWaard, J. R. Biological identifications through DNA barcodes Proc. R. Soc. London, Ser. B. 2003, 270, 313-321 (Pubitemid 36228536)
13. Colombo, F; Chessa, S; Cattaneo, P; Bernardi, C. Polymerase chain reaction products (PCR) on "DNA barcode zone" resolved by temporal temperature gradient electophoresis: A tool for species identification of mixed meat specimens-A technical note on preliminary results Food Control 2010, 22 (8) 1471-1472
14. Handy, S. M.; Deeds, J.; Ivanova, N.; Hebert, P.; Hanner, R.; Ormos, A; Weigt, L.; Moore, M.; Yancy, H. A single laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance J. AOAC Int. 2011, 94, 1
15. Rasmussen-Hellberg, R.; Naaum, A.; Handy, S. M.; Hanner, R.; Yancy, H.; Deeds, J.; Morrissey, M. Interlaboratory evaluation of a real-time multiplex polymerase chain reaction method for identification of salmon and trout species in commercial products J. Agric. Food Chem. 2011, 59, 876-884
16. Fazekas, A. J.; Burgess, K. S.; Kesanakurti, P. R.; Graham, S. W.; Newmaster, S. G.; Husband, B. C.; Percy, D. M.; Hajibabaei, M.; Barrett, S. C. H. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well PLoS One 2008, 3 (7) e2802
17. Hollingsworth, P. M.; Forrest, L. L.; Spouge, J. L. CBOL Plant Working Grp. A DNA barcode for land plants Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (31) 12794-12797
18. Chen, S.; Yao, H.; Han, J.; Liu, C.; Song, J.; Shi, L.; Zhu, Y.; Ma, X.; Gao, T.; Pang, X.; Luo, K.; Li, Y.; Li, X.; Jia, X.; Lin, Y.; Leon, C. Validation of the ITS2 Region as a novel DNA barcode for identifying medicinal plant species. PLoS One 2010, 5 (1).
19. Pennisi, E. Wanted: A barcode for plants Science 2007, 318, 190-191
20. Gernandt, D. S.; Lopez, G.; Garcia, S. O.; Liston, A. Phylogeny and classification of Pinus Taxon 2005, 54, 29-42 (Pubitemid 40440894)
21. Whittall, J. B.; Syring, J.; Parks, M.; Buenrostro, J.; Dick, C.; Liston, A.; Cronn, R. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines Mol. Ecol. 2010, 19 (Suppl. 1) 100-114
22. Farjon, A. Pines: Drawings and descriptions of the genus Pinus, 2 nd ed.; Koninklijke Brill NV: Leiden, The Netherlands, 2005; pp 232-235.
23. Ran, J. H.; Wang, P. P.; Zhao, H. J.; Wang, X. Q. A test of seven candidate barcode regions from the plastome in Picea (Pinaceae) J. Integr. Plant Biol. 2010, 52 (12) 1109-1126
24. Parks, M.; Liston, A.; Cronn, R. Newly developed primers for complete YCF1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility Am. J. Bot. 2011, 98 (7) e185-e188
25. Drummond, A. J.; Ashton, B.; Buxton, S.; Cheung, M.; Cooper, A.; Heled, J.; Kearse, M.; Moir, R.; Stones-Havas, S.; Sturrock, S.; Thierer, T; Wilson, A. Geneious v5.1, available from http://www.geneious.com, 2010.
26. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 2004, 32, 1792-1797 (Pubitemid 38832724)
27. Jukes, T. H.; Cantor, C. R. Evolution of protein molecules. In Mammalian protein metabolism; Munro, H. N., Ed.; Academic Press: New York, 1969; pp 21-123.
28. Saitou, N.; Nei, M. The neighbor-joining method: a new method for reconstruction phylogenetic trees Mol. Biol. Evol. 1987, 4, 406-425
29. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol. Biol. Evol. 2000, 17, 540-552 (Pubitemid 30210700)
30. Parks, M.; Cronn, R.; Liston, A. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes BMC Biol. 2009, 7 (1) 84
31. Neubig, K. M.; Whitten, W. M.; Carlsward, B. S.; Blanco, M. A.; Endara, L.; Williams, N. H.; Moore, M. Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK Plant Syst. Evol. 2009, 277 (1-2) 75-84
32. Hollingsworth, P. M.; Graham, S. W.; Little, D. P. Choosing and Using a Plant DNA Barcode PLoS ONE. 2011, 6 (5) e19254
33. Li, D.-Z.; Liu, J.-Q.; Chen, Z.-D.; Wang, H.; Ge, X.-J.; Zhou, S.-L.; Gao, L.-M.; Fu, C.-X.; Chen, S.-L. Plant DNA barcoding in China J. Syst. Evol. 2011, 49 (3) 169-175