Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Ganopoulos, Ioannis ^a,b   Aravanopoulos, Filippos ^a,b   Madesis, Panagiotis ^a   Pasentsis, Konstantinos ^a   Bosmali, Irene ^a   Ouzounis, Christos ^a,c   Tsaftaris, Athanasios ^a,b  

^a INFORMATION TECHNOLOGIES INSTITUTE   (Greece)

^b ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIODIVERSITY; CONTROLLED STUDY; DNA BARCODING; DNA DETERMINATION; DNA FINGERPRINTING; DNA SEQUENCE; EXTRACHROMOSOMAL INHERITANCE; GENE; GENETIC MARKER; GENETIC VARIABILITY; HIGH RESOLUTION MELTING ANALYSIS; HYBRID; NONHUMAN; PHENOTYPE; PINE; PINUS NIGRA; PLANT LEAF; POLYMERASE CHAIN REACTION; SCOTS PINE; SOUTHERN EUROPE; TAXONOMIC IDENTIFICATION; TRNL GENE;

CLASSIFICATION; CYTOPLASM; DNA BARCODING, TAXONOMIC; DNA, PLANT; GENETIC MARKERS; HYBRIDIZATION, GENETIC; INTRONS; PINUS; PLASTIDS; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TIME FACTORS; TRANSITION TEMPERATURE; WOOD;

PINUS BRUTIA; PINUS HALEPENSIS; PINUS NIGRA; PINUS SYLVESTRIS;

EID: 84875947453     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060945     Document Type: Article

References (73)

1. Farjon A (2001) World checklist and bibliography of conifers: Royal Botanic Gardens, Kew, UK.
2. Plomion C, Chagné D, Pot D, Kumar S, Wilcox P, et al. (2007) Pines. In: Kole C, editor. Forest Trees: Springer Berlin Heidelberg. 29-92.
3. Barbero M, Loisel R, Quezel P, Richardson MD, Romane F (2000) Pines of the Mediterranean basin; Richardson DM, editor. Cambridge, Cambridge University Press.
4. Le Maitre D (1998) Pines in cultivation: a global view. Cambridge, Cambridge University Press.
5. Little DP, Stevenson DW, (2007) A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23: 1-21.
6. Mirov NT (1967) The Genus Pinus. New York: Ronald Press.
7. Gernandt DS, Hernandez-Leon S, Salgado-Hernandez E, de la Rosa JAP, (2009) Phylogenetic Relationships of Pinus Subsection Ponderosae Inferred from Rapidly Evolving cpDNA Regions. Systematic Botany 34: 481-491.
8. Gernandt DS, López GG, García SO, Aaron L, (2005) Phylogeny and Classification of Pinus. Taxon 54: 29-42.
9. Little EL, Critchfield WB (1969) Subdivisions of the Genus Pinus (Pines); Pub UFSM, editor.
10. Eckert AJ, Hall BD, (2006) Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): Phylogenetic tests of fossil-based hypotheses. Molecular Phylogenetics and Evolution 40: 166-182.
11. Price A, Liston A, Straus SH (2000) Phylogeny and systematics of Pinus; (ed) IRD, editor. Cambridge, Cambridge University Press.
12. Straus SH, Doerksen AH, (1990) Restriction fragment analysis of Pine phylogeny. Evolution 44: 1081-1096.
13. Neale DB, Sederoff RR, (1989) Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. TAG Theoretical and Applied Genetics 77: 212-216.
14. Geada Lopez G, Kamiya K, Harada K (2002) Phylogenetic relationships of Diploxylon pines (subgenus Pinus) based on plastid sequence data. Chicago, IL: University of Chicago Press. 11p.
15. Wang X-R, Szmidt AE, Nguyên HN, (2000) The phylogenetic position of the endemic flat-needle pine; Pinus krempfii; (Pinaceae) from Vietnam, based on PCR-RFLP analysis of chloroplast DNA. Plant Systematics and Evolution 220: 21-36.
16. Liston A, Robinson WA, Piñero D, Alvarez-Buylla ER, (1999) Phylogenetics of Pinus (Pinaceae) Based on Nuclear Ribosomal DNA Internal Transcribed Spacer Region Sequences. Molecular Phylogenetics and Evolution 11: 95-109.
17. Neophytou C, Aravanopoulos FA, Fink S, Dounavi A, (2010) Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Q. robur L.) using small sets of microsatellite markers. Forest Ecology and Management 259: 2026-2035.
18. Sun M, Lo EYY, (2011) Genomic markers reveal introgressive hybridization in the Indo-West pacific mangroves: A Case Study. PLoS ONE 6: e19671.
19. Finkeldey R, Leinemann L, Gailing O, (2010) Molecular genetic tools to infer the origin of forest plants and wood. Applied Microbiology and Biotechnology 85: 1251-1258.
20. Deguilloux M-F, Pemonge M-Hln, Petit RmJ, (2004) DNA-based control of oak wood geographic origin in the context of the cooperage industry. Ann For Sci 61: 97-104.
21. Wong KN, Tan WL, Chew FT, (2009) Identification and characterization of microsatellite loci in Intsia palembanica (Leguminosae), a valuable tropical timber species. Molecular Ecology Resources 9: 360-364.
22. Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, et al. (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 106: 12794-12797.
23. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH, (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102: 8369-8374.
24. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, et al. (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 35:-.
25. Vijayan K, Tsou C, (2010) DNA barcoding in plants: taxonomy in a new perspective. Current Science 99: 1530-1541.
26. de Groot GA, During HJ, Maas JW, Schneider H, Vogel JC, et al. (2011) Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: An ecological perspective. PLoS ONE 6: e16371.
27. Ganopoulos I, Madesis P, Darzentas N, Argiriou A, Tsaftaris A (2012) Barcode High Resolution Melting (Bar-HRM) analysis for detection and quantification of PDO "Fava Santorinis" (Lathyrus clymenum) adulterants. Food Chemistry Accepted.
28. Olivieri C, Marota I, Rollo F, Luciani S, (2012) Tracking Plant, Fungal, and Bacterial DNA in Honey Specimens. Journal of Forensic Sciences 57: 222-227.
29. Spaniolas S, Bazakos C, Spano T, Zoghby C, Kalaitzis P, (2010) The potential of plastid trnL (UAA) intron polymorphisms for the identification of the botanical origin of plant oils. Food Chemistry 122: 850-856.
30. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, et al. (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE 3.
31. Sass C, Little DP, Stevenson DW, Specht CD, (2007) DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of Cycads. PLoS ONE 2: e1154.
32. Ran J-H, Wang P-P, Zhao H-J, Wang X-Q, (2010) A test of seven candidate barcode regions from the plastome in Picea (Pinaceae). Journal of Integrative Plant Biology 52: 1109-1126.
33. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ, (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49: 853-860.
34. Wittwer CT, (2009) High-resolution DNA melting analysis: advancements and limitations. Hum Mutat 30: 857-859.
35. Zhou L, Wang L, Palais R, Pryor R, Wittwer CT, (2005) High-resolution DNA melting analysis for simultaneous mutation scanning and genotyping in solution. Clin Chem 51: 1770-1777.
36. Reed GH, Kent JO, Wittwer CT, (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8: 597-608.
37. Ganopoulos I, Argiriou A, Tsaftaris A, (2011) Microsatellite high resolution melting (SSR-HRM) analysis for authenticity testing of protected designation of origin (PDO) sweet cherry products. Food Control 22: 532-541.
38. Ganopoulos I, Argiriou A, Tsaftaris A, (2011) Adulterations in Basmati rice detected quantitatively by combined use of microsatellite and fragrance typing with High Resolution Melting (HRM) analysis. Food Chemistry 129: 652-659.
39. Jaakola L, Suokas M, Häggman H, (2010) Novel approaches based on DNA barcoding and high-resolution melting of amplicons for authenticity analyses of berry species. Food Chemistry 123: 494-500.
40. Theodoropoulos K, Eleftheriadou E, Gerasimidis A (2004) The Forest Botanic Garden (Arboretum) at the Aristotle University of Thessaloniki. Greece In: International Scientific Symposium "Botanic Gardens: Awareness for Biodiversity", Botanic Garden and Botanical Museum Berlin-Dahlem, Germany 37-38.
41. Moulalis D, Panetsos K, Scaltsoyiannes A, Aravanopoulos F, Tsaktsira M, et al. (1998) Identification and production of F1 artificial hybrids between brutia and Aleppo pines. In: Proc 8th Pan-Hellenic Forest Scientific Society Conf, Geotechnical Chamber of Greece Publ, Thessaloniki, 354-360.
42. Rachmayanti Y, Leinemann L, Gailing O, Finkeldey R, (2006) Extraction, amplification and characterization of wood DNA from Dipterocarpaceae. Plant Molecular Biology Reporter 24: 45-55.
43. Rachmayanti Y, Leinemann L, Gailing O, Finkeldey R, (2009) DNA from processed and unprocessed wood: Factors influencing the isolation success. Forensic Science International: Genetics 3: 185-192.
44. Hewson K, Noormohammadi A, Devlin J, Mardani K, Ignjatovic J, (2009) Rapid detection and non-subjective characterisation of infectious bronchitis virus isolates using high-resolution melt curve analysis and a mathematical model. Archives of Virology 154: 649-660.
45. Dwight Z, Palais R, Wittwer CT, (2011) uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. Bioinformatics 27: 1019-1020.
46. Waterhouse AM, Procter JB, Martin DMA, Clamp Ml, Barton GJ, (2009) Jalview Version 2. A multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
47. Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H, (2008) Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society B: Biological Sciences 275: 237-247.
48. Rozas J, Sanchez-Del Barrio JC, Messeguer X, Rozas R, (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
49. Ewing B, Hillier L, Wendl MC, Green P, (1998) Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment. Genome Research 8: 175-185.
50. Gordon D (2002) Viewing and Editing Assembled Sequences Using Consed. Current Protocols in Bioinformatics: John Wiley & Sons, Inc.
51. Little DP, (2010) A unified index of sequence quality and contig overlap for DNA barcoding. Bioinformatics 26: 2780-2781.
52. Jeffery N, Gasser RB, Steer PA, Noormohammadi AH, (2007) Classification of Mycoplasma synoviae strains using single-strand conformation polymorphism and high-resolution melting-curve analysis of the vlhA gene single-copy region. Microbiology 153: 2679-2688.
53. Robertson T, Bibby S, O'Rourke D, Belfiore T, Lambie H, et al. (2009) Characterization of Chlamydiaceae species using PCR and high resolution melt curve analysis of the 16S rRNA gene. Journal of Applied Microbiology 107: 2017-2028.
54. Reed GH, Wittwer CT, (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 50: 1748-1754.
55. Erali M, Voelkerding KV, Wittwer CT, (2008) High resolution melting applications for clinical laboratory medicine. Exp Mol Pathol 85: 50-58.
56. Cheng J-C, Huang C-L, Lin C-C, Chen C-C, Chang Y-C, et al. (2006) Rapid Detection and Identification of Clinically Important Bacteria by High-Resolution Melting Analysis after Broad-Range Ribosomal RNA Real-Time PCR. Clinical Chemistry 52: 1997-2004.
57. Mackay JF, Wright CD, Bonfiglioli RG, (2008) A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars. Plant Methods 4: 8.
58. Mader E, Lukas B, Novak J, (2008) A strategy to setup codominant microsatellite analysis for high-resolution-melting-curve-analysis (HRM). BMC Genet 9: 69.
59. Stephens AJ, Inman-Bamber J, Giffard PM, Huygens F, (2008) High-Resolution Melting analysis of the spa repeat region of Staphylococcus aureus. Clinical Chemistry 54: 432-436.
60. Strid A, Tan K (1997) Flora Hellenica. Konigstein.
61. Panetsos K, Scaltsoyiannes A, Aravanopoulos FA, Dounavi K, Demetrakopoulos A (1997) Identification of Pinus brutia TEN., P. halepensis MILL. and their putative hybrids. Silvae Genetica 46.
62. Aravanopoulos FA, Drouzas AD, Wang XR, Panetsos KP, Moulalis D, (2000) Preliminary results on the inheritance of the chloroplast genome in Pinus brutia Ten. In: Gozukirmizi, N, (ed) Proc 2nd Balkan Botanical Congress, Istanbul, Turkey, May 14-18, 2000, Vol 2: 195-200.
63. Bucci G, Anzidei M, Madaghiele A, Vendramin GG, (1998) Detection of haplotypic variation and natural hybridization in Halepensis-complex pine species using chloroplast simple sequence repeat (SSR) markers. Molecular Ecology 7: 1633-1643.
64. Frankis M, (1999) Plate 367. Pinus brutia. Curtis's Botanical Magazine 16: 173-184.
65. Ren B-Q, Xiang X-G, Chen Z-D, (2010) Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers. Molecular Ecology Resources 10: 594-605.
66. Chen JC, Tauer CT, Huang YH, (2002) Paternal chloroplast inheritance patterns in pine hybrids detected with trnL-trnF intergenic region polymorphism. Theoretical and Applied Genetics 104: 1307-1311.
67. White T, Adams W, Neale D (2007) Forest Genetics. Cambridge: CABI Publisher.
68. Deguilloux M, Pemonge M, Petit R, (2002) Novel perspectives in wood certification and forensics: dry wood as a source of DNA. Proceedings of the Royal Society of London Series B: Biological Sciences 269: 1039-1046.
69. Yoshida K, Kagawa A, Nishiguchi M (2007) Extraction and detection of DNA from wood for species identification. Proceedings of the International Symposium on Development of Improved Methods to Identify Shorea Species Wood and its Origin: 27-34.
70. Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, et al. (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-166.
71. Ronning SB, Rudi K, Berdal KG, Holst-Jensen A, (2005) Differentiation of important and closely related cereal plant species (Poaceae) in food by hybridization to an oligonucleotide array. Journal of Agricultural and Food Chemistry 53: 8874-8880.
72. Ward J, Peakall R, Gilmore SR, Robertson J, (2005) A molecular identification system for grasses: a novel technology for forensic botany. Forensic Science International 152: 121-131.
73. Papajoannou J, (1936) Eine new varietät von Pinus brutia Ten., Pinus brutia Ten. var. agrophiotii. Extrait des Praktika de l'Académie d'Athènes 11: 14-24.