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DNA Fingerprinting, DNA Barcoding, and Next Generation Sequencing Technology in Plants

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Plant DNA Fingerprinting and Barcoding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 862))

Abstract

DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in “next generation sequencing” (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of “NGS” technology for DNA fingerprinting and DNA barcoding applications.

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References

  1. Herschel WJ (1880) Skin Furrows of the Hand. Nature 23:76

    Google Scholar 

  2. Jeffreys AJ, Wilson V, and Thein SL (1985) Individual-specific ‘fingerprints’ of human DNA. Nature 316(6023):76–79

    Article  PubMed  CAS  Google Scholar 

  3. Galton F (1892) Finger prints. Macmillan and Co., New York

    Google Scholar 

  4. Hawass Z, Gad YZ, Ismail S, et al (2010) Ancestry and Pathology in King Tutankhamun’s Family. JAMA 303(7):638–647

    Article  PubMed  CAS  Google Scholar 

  5. Weising K (2005) DNA fingerprinting in plants: principles, methods, and applications. Taylor & Francis Group, Boca Raton

    Book  Google Scholar 

  6. Bartlett J and Stirling D (2003) A short history of the polymerase chain reaction. In: Bartlett J & Stirling D (ed) Methods in molecular biology: PCR protocols, 2nd edn. Humana Press Inc., Totowa

    Chapter  Google Scholar 

  7. Hebert PD, Cywinska A, Ball SL, et al (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270(1512):313–321

    Article  PubMed  CAS  Google Scholar 

  8. Chase MW, Cowan RS, Hollingsworth PM, et al (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56(2):295–299

    Google Scholar 

  9. Hollingsworth P, Forrest L, Spouge J, et al (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797

    Article  CAS  Google Scholar 

  10. Smith LM, Sanders JZ, Kaiser RJ, et al (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321(6071): 674–679

    Article  PubMed  CAS  Google Scholar 

  11. Shendure J and Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145

    Article  PubMed  CAS  Google Scholar 

  12. Oetting WS (2010) Impact of next generation sequencing: the 2009 Human Genome Variation Society Scientific Meeting. Hum Mutat 31(4):500–503

    Article  PubMed  Google Scholar 

  13. Imelfort M and Edwards D (2009) De novo sequencing of plant genomes using second-generation technologies. Briefings in Bioinformatics 10(6):609–618

    Article  PubMed  CAS  Google Scholar 

  14. Zhang J, Chiodini R, Badr A, et al (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38(3):95–109

    Article  PubMed  Google Scholar 

  15. Varshney RK, Nayak SN, May GD, et al (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27(9):522–530

    Article  PubMed  CAS  Google Scholar 

  16. You FM, Huo N, Deal KR, et al (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 12:59

    Article  PubMed  CAS  Google Scholar 

  17. Magbanua ZV, Ozkan S, Bartlett BD, et al (2011) Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS ONE 6(1):e16214

    Article  PubMed  CAS  Google Scholar 

  18. Steuernagel B, Taudien S, Gundlach H, et al (2009) De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 10:547

    Article  PubMed  Google Scholar 

  19. Straub S, Fishbein M, Livshultz T, et al (2011) Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 12(1):211

    Article  PubMed  CAS  Google Scholar 

  20. Nature (2011) Reviews glossary. Nature. http://www.nature.com/nrg/journal/v6/n11/glossary/nrg1709_glossary.html. Accessed 21 June 2011

  21. Ronaghi M, Uhlen M, and Nyren P (1998) A sequencing method based on real-time pyrophosphate. Science 281(5375):363–365

    Article  PubMed  CAS  Google Scholar 

  22. Ronaghi M, Karamohamed S, Pettersson B, et al (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242(1):84–89

    Article  PubMed  CAS  Google Scholar 

  23. Parchman TL, Geist KS, Grahnen JA, et al (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180

    Article  PubMed  Google Scholar 

  24. Illumina (2010) Technology Spotlight: Illumina® Sequencing.

    Google Scholar 

  25. Huang S, Li R, Zhang Z, et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41(12):1275–1281

    Article  PubMed  CAS  Google Scholar 

  26. Velasco R, Zharkikh A, Troggio M, et al (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLoS ONE 2(12):e1326

    Article  PubMed  Google Scholar 

  27. Shinozaki K, Ohme M, Tanaka M, et al (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5(9):2043–2049

    PubMed  CAS  Google Scholar 

  28. Nock CJ, Waters DLE, Edwards MA, et al (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnology Journal 9(3):328–333

    Article  PubMed  CAS  Google Scholar 

  29. Parks M, Cronn R, and Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology 7(1):84

    Article  PubMed  Google Scholar 

  30. Meyer M, Stenzel U, and Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3(2):267–278

    Article  PubMed  CAS  Google Scholar 

  31. Cronn R, Liston A, Parks M, et al (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e122

    Article  PubMed  Google Scholar 

  32. Doorduin L, Gravendeel B, Lammers Y, et al (2011) The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Res 18(2):93–105

    Article  PubMed  CAS  Google Scholar 

  33. Sønstebø JH, Gielly L, Brysting AK, et al (2010) Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources 10(6):1009–1018

    Article  PubMed  Google Scholar 

  34. Gardner MG, Fitch AJ, Bertozzi T, et al (2011) Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources. doi:10.1111/j.1755-0998.2011.03037.x

  35. Michalczyk IM, Schumacher C, Mengel C, et al (2011) Identification and characterization of 12 microsatellite loci in Cnidium dubium (Apiaceae) using next-generation sequencing. American Journal of Botany 98(5):e127–e129

    Article  PubMed  CAS  Google Scholar 

  36. Buehler D, Graf R, Holderegger R, et al (2011) Using the 454 pyrosequencing-based technique in the development of nuclear microsatellite loci in the alpine plant Arabis alpina (Brassicaceae). American Journal of Botany 98(5):e103–e105

    Article  CAS  Google Scholar 

  37. Delmas CEL, Lhuillier E, Pornon A, et al (2011) Isolation and characterization of microsatellite loci in Rhododendron ferrugineum (Ericaceae) using pyrosequencing technology. American Journal of Botany 98(5):e120–e122

    Article  PubMed  CAS  Google Scholar 

  38. Csencsics D, Brodbeck S, and Holderegger R (2010) Cost-Effective, Species-Specific Microsatellite Development for the Endangered Dwarf Bulrush (Typha minima) Using Next-Generation Sequencing Technology. Journal of Heredity 101(6):789–793

    Article  PubMed  CAS  Google Scholar 

  39. Marroni F, Pinosio S, Di Centa E, et al (2011) Large scale detection of rare variants via pooled multiplexed next generation sequencing: towards next generation Ecotilling. The Plant Journal. doi:10.1111/j.1365-313X.2011.04627.x

  40. Myles S, Chia J-M, Hurwitz B, et al (2010) Rapid Genomic Characterization of the Genus Vitis. PLoS ONE 5(1):e8219

    Article  PubMed  Google Scholar 

  41. Barbazuk WB and Schnable PS (2011) SNP Discovery by Transcriptome Pyrosequencing. cDNA Libraries 729:225–246

    Google Scholar 

  42. Arai-Kichise Y, Shiwa Y, Nagasaki H, et al (2011) Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing. Plant and Cell Physiology 52(2):274–282

    Article  PubMed  CAS  Google Scholar 

  43. Hyten D, Song Q, Fickus E, et al (2010) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11(1):475

    Article  PubMed  Google Scholar 

  44. Griffin PC, Robin C, and Hoffmann AA (2011) A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol 9:19

    Article  PubMed  CAS  Google Scholar 

  45. Elshire RJ, Glaubitz JC, Sun Q, et al (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE 6(5):e19379

    Article  PubMed  CAS  Google Scholar 

  46. Lister R, Gregory BD, and Ecker JR (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Current Opinion in Plant Biology 12(2):107–118

    Article  PubMed  CAS  Google Scholar 

  47. Molina C, Zaman-Allah M, Khan F, et al (2011) The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE. BMC Plant Biology 11(1):31

    Article  PubMed  CAS  Google Scholar 

  48. Hiremath PJ, Farmer A, Cannon SB, et al (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnology Journal:10.1111/j.1467-7652.2011.00625.x

  49. Severin A, Woody J, Bolon Y-T, et al (2010) RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. BMC Plant Biology 10(1):160

    Article  PubMed  Google Scholar 

  50. Lu T, Lu G, Fan D, et al (2010) Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Research 20(9):1238–1249

    Article  PubMed  CAS  Google Scholar 

  51. Franssen S, Shrestha R, Brautigam A, et al (2011) Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics 12(1):227

    Article  PubMed  CAS  Google Scholar 

  52. Angeloni F, Wagemaker CAM, Jetten MSM, et al (2011) De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques. Molecular Ecology Resources 11(4):662–674

    Article  PubMed  CAS  Google Scholar 

  53. Wei LQ, Yan LF, and Wang T (2011) Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol 12(6):R53

    Article  PubMed  CAS  Google Scholar 

  54. Zhao C-Z, Xia H, Frazier T, et al (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biology 10(1):3

    Article  PubMed  Google Scholar 

  55. Mohorianu I, Schwach F, Jing R, et al (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. The Plant Journal. doi:10.1111/j.1365-313X.2011.04586.x

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Authors and Affiliations

  1. Department of Science, Technology, Engineering & Math (S.T.E.M.), Roxbury Community College, Roxbury Crossing, Boston, MA, USA

    Nikolaus J. Sucher

  2. Centre for Complementary Medicine Research, School of Science and Health, University of Western Sydney, Penrith, NSW, Australia

    James R. Hennell

  3. Department of Natural Sciences, Northern Essex Community College, Haverhill, MA, USA

    Maria C. Carles

Authors
  1. Nikolaus J. Sucher
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  2. James R. Hennell
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  3. Maria C. Carles
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Corresponding author

Correspondence to Nikolaus J. Sucher .

Editor information

Editors and Affiliations

  1. , Department of S.T.E.M., Roxbury Community College, Columbus Avenue 1234, Roxbury Crossing, 02120, Massachusetts, USA

    Nikolaus J. Sucher

  2. Centre for Complementary Medicine, Research, University of Western Sydney, Narellan Road, Campbelltown, 2560, New South Wales, Australia

    James R. Hennell

  3. , Department of Natural Sciences, Northern Essex Community College, Elliot Street 110, Haverhill, 01830, Massachusetts, USA

    Maria C. Carles

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Sucher, N.J., Hennell, J.R., Carles, M.C. (2012). DNA Fingerprinting, DNA Barcoding, and Next Generation Sequencing Technology in Plants. In: Sucher, N., Hennell, J., Carles, M. (eds) Plant DNA Fingerprinting and Barcoding. Methods in Molecular Biology, vol 862. Humana Press. https://doi.org/10.1007/978-1-61779-609-8_2

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  • DOI: https://doi.org/10.1007/978-1-61779-609-8_2

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-608-1

  • Online ISBN: 978-1-61779-609-8

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