How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Särkinen, Tiina ^a,b   Staats, Martijn ^c   Richardson, James E ^a,d   Cowan, Robyn S ^e   Bakker, Freek T ^c  

^a ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d UNIVERSIDAD DE LOS ANDES   (Colombia)

^e ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; PLANT DNA;

AMPLICON; ARTICLE; DNA BARCODING; DNA EXTRACTION; DNA SEQUENCE; EXON; GENE AMPLIFICATION; NONHUMAN; POLYMERASE CHAIN REACTION;

BIODIVERSITY; CHEMICAL FRACTIONATION; DESICCATION; DNA, PLANT; DNA-DIRECTED DNA POLYMERASE; PHYLOGENY; PLANTS; POLYMERASE CHAIN REACTION; PRESERVATION, BIOLOGICAL; SILICON DIOXIDE;

EID: 84865464866     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043808     Document Type: Article

References (49)

1. Medellín-Leal F, (1975) Origenes, desarrollo historico y estado actual de los herbarios en el mundo. Bol Soc Bot Mex 1975 34: 3-26.
2. Sheltler SG, (1969) The herbarium: Past, present, and future. Proc Biol Soc Amer 82: 687-758.
3. Holmgren PK, Holmgren NH, Barnett LC (1990) Index herbariorum. Part I: The herbaria of the world. New York: New York Botanical Garden. 693 p.
4. Bebber DP, Carine MA, Wood JRI, Wortley AH, Harris DJ, et al. (2010) Herbaria are a major frontier for species discovery. Proc Natl Acad Sci USA 107: 22169-22171.
5. Joppa LN, Roberts DL, Pimm SL, (2011) How many species of flowering plants are there? Proc Biol Sci 278: 554-559.
6. Staats M, Cuenca A, Richardson JE, Vrielink-van Ginkel R, Petersen G, et al. (2011) DNA damage in plant herbarium tissue. PLoS ONE 6: e28448.
7. Harris SA, (1993) DNA analysis of tropical plant species: an assessment of different drying methods. P1ant Syst Evol 188: 57-64.
8. Pyle MM, Adams RP, (1989) In situ preservation of DNA in plant specimens. Taxon 38: 576-581.
9. Erkens RHJ, Cross H, Maas JW, Hoenselaar K, Chatrou LW, (2008) Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA. Blumea 53: 407-428.
10. Weising K, Nybom H, Wolff K, Meyer W (1995) DNA fingerprinting in plants and fungi. Boca Raton: CRC Press. p.322.
11. Doyle JJ, Dickson EE, (1987) Preservation of plant species for DNA restriction endonuclease analysis. Taxon 36: 715-722.
12. Jobes DV, Hurley DL, Thien LB, (1995) Plant DNA isolation: a method to efficiently remove polyphenolics, polysaccharides and RNA. Taxon 44: 379-386.
13. Barnwell P, Blanchard AN, Bryant JA, Smirnoff N, Weir AF, (1998) Isolation of DNA from the highly mucilagenous succulent plant Sedum telephium. Plant Mol Biol Rep 16: 133-138.
14. de la Cruz M, Ramirez F, Hernandez H, (1997) DNA isolation and amplification from cacti. Plant Mol Biol Rep 15: 319-325.
15. Al-Shayji Y, Saleem M, Al-Amad S, Al-Awadhi S, Al-Salameen F, (2004) Isolation and analysis of the total genomic DNA from the date palm (P. dactylifera L.) and related species. Acta Biotechnologica 14: 163-168.
16. Fleischmann A, Heubl G, (2009) Overcoming DNA extraction problems from carnivorous plants. An Jard Bot Madrid 66: 209-215.
17. Michiels A, Van den Ende W, Tucker M, Van Riet L, Van Laere A, (2003) Extraction of high-quality genomic DNA from latex-containing plants. Anal Biochem 315: 85-89.
18. Rogers SO, Bendich AJ, (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol Biol 5: 69-76.
19. Savolainen V, Cuénoud P, Spichiger R, Martinez MDP, Crèvecoeur M, et al. (1995) The use of herbarium specimens in DNA phylogenetics: evaluation and improvement. Plant Syst Evol 197: 87-98.
20. Drábková L, Kirschner J, Vleek C, (2002) Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. Plant Mol Biol Rep 20: 161-175.
21. Jankowiak K, Buczkowska K, Szweykowska-Kulinska Z, (2005) Successful extraction of DNA from 100-year-old herbarium specimens of the liverwort Bazzania trilobata. Taxon 54: 335-336.
22. Li F-W, Kuo L-Y, Huang Y-M, Chiou W-L, Wang C-N, (2010) Tissue-direct PCR, a rapid and extraction-free method for barcoding of ferns. Mol Ecol Res 10: 92-95.
23. Brockington SF, Mavrodiev E, Famdial J, Dhingra A, Soltis PS, et al. (2008) Keep the DNA rolling: multiple displacement amplification of archival plant DNA extracts. Taxon 57: 944-948.
24. Pan X, Urban AE, Palejev D, Schulz V, Grubert F, et al. (2008) A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc Natl Acad Sci USA 105: 15499-15504.
25. Ivanova NV, Fazekas AJ, Hebert PDN, (2008) Semi-automated, membrane-based protocol for DNA isolation from plants. Plant Mol Biol Rep 26: 186-198.
26. Doyle JJ, Doyle JL, (1987) A rapid isolation procedure for small quantities of fresh leaf material. Phytochem Bull 19: 11-15.
27. Höss M, Pääbo S, (1993) DNA extraction from Pleistocene bones by a silica-based purification method. Nucl Acids Res 21: 3913-3914.
28. Hänni C, Brousseau T, Laudet V, Stehelin D, (1995) Isopropanol precipitation removes PCR inhibitors from ancient bone extracts. Nucleic Acids Res 23: 881-882.
29. Kalmar T, Bachrati CZ, Marcsik A, Rasko I, (2000) A simple and efficient method for PCR amplifiable DNA extraction from ancient bones. Nucl Acids Res 28: E67.
30. Rohland N, Hofreiter M, (2007b) Ancient DNA extraction from bones and teeth. Nature Protocols 2: 1756-1762.
31. Soltis PS, Soltis DE, (1993) Ancient DNA: prospects and limitations. New Zealand J Bot 31: 203-209.
32. Zimmermann J, Hajibabaei M, Blackburn DC, Hanken J, Cantin E, et al. (2008) DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers of Zoology 5: doi:10.1186/1742-9994-5-18.
33. Telle S, Thines M, (2008) Amplification of cox2 (~620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases. PLoS ONE 3: e3584.
34. Rohland N, Hofreiter M, (2007a) Comparison and optimization of ancient DNA extraction. BioTechniques 42: 343-352.
35. Pääbo S (1990) Amplifying ancient DNA. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. New York: Academic Press. 159-166.
36. Schenck H, (1887) Instrumente, Präparationsmethoden - Ueber die Schweinfurth'sche Methode, Pflanzen für Herbarien auf Reisen zu conserviren. Botanisches Centralblatt 35: 175-176.
37. Schenck H (1888) Schweinfurth's method for preserving plants. Bull Torrey Bot Club: 292-293.
38. Schenck H (1889) Schweinfurth's method for preserving plants. Kew Bull: 19-20.
39. Taberlet P, Coissac E, Pompanon FO, Brochmann C, Willerslev E, (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21: 2045-2050.
40. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, et al. (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes 6: 959-964.
41. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106: 12794-12797.
42. Raye G, Miquel C, Coissac E, Redjadj C, Loison A, et al. (2011) New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study. Ecol Research 26: 265-276.
43. Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, et al. (2009) Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front Zoo 6: DOI:10.1186/1742-9994-6-16.
44. Hofreiter M, HN Poinar, WG Spaulding, K Bauer, PS Martin, et al. (2000) A molecular analysis of ground sloth diet through the last glaciation. Mol Ecol 9: 1975-1984.
45. 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. Nucl Acids Res 35: e14.
46. Metzker ML, (2010) Sequencing technologies - the next generation. Nature Reviews Genetics 11: 31-46.
47. Thompson JF, Milos PM, (2011) The properties and applications of single-molecule DNA sequencing. Genome Biol 12: 217.
48. Kress WJ, Erickson DL, (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2: e508.
49. Frohlich MW, Meyerowitz EM, (1997) The search for flower homeotic gene homologs in basal angiosperms and gnetales: a potential new source of data on the evolutionary origin of flowers. Int J Plant Sci 158: S131-S142.