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DNA Barcoding and Phylogenetic Analysis of Plant Species: Urban Barcode Project of New York City

Authors(4):

Irving Estevez, Stephen Mensah, Rujin Tian, Martin Fein
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DNA barcoding relies on the use of a standardized DNA region as a tag for simple, rapid and affordable species identification. To get hands-on experience on species identification using molecular tools and to explore the genetic biodiversity of New York City, we participated in the Urban Barcoding Project conducted by the DNA Learning Center of Cold Spring Harbor Lab (CSHL). The gene region that is proposed as the standard barcode for plants by CSHL is a ~600 base pair fragment from the RuBisCo (ribulose bisphosphate carboxylase/oxygenase) large subunit (rbcL) located in the chloroplast. We began our investigation by collecting and selecting a total of 10 native plant specimens located in the campus of the Bronx Community College of New York City with the help of two mobile apps (Google Maps and Garden Compass). Next, we successfully optimized the protocols provided by the CSHL to achieve DNA purification, rbcL amplification and sequencing. Finally, we applied bioinformatic tools (sequence alignment; substitution rate and time computation; 3D structure comparison) for DNA-based species identification, protein structure homology modeling and phylogenetic analysis. Our research experience helped us develop a greater appreciation for the DNA sequence based modern taxonomy in urban environments while gaining an introduction to bioinformatics tools.

Irving Estevez, Stephen Mensah, Rujin Tian, Martin Fein

DNA Barcoding, Garden Compass App, Phylogeny, Protein Superimposition, rbcl, Sequence Alignment, Species Identification

  1. Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36
  2. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, Mar 19;32(5):1792-7.
  3. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, Apr;17(4):540-52.
  4. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New Algorithms and Methods to
  5. Anisimova M., Gascuel O. Approximate likelihood ratio test for branches: A fast, accurate and powerful alternative. Syst Biol. 2006, Aug;55(4):539-52.
  6. Chevenet F., Brun C., Banuls AL., Jacq B., Chisten R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics. 2006, Oct 10;7:439.
  7. Xiang Z. Advances in homology protein structure modeling. Curr Protein Pept Sci. 2006 Jun;7(3):217-27.
  8. Rosenzweig ML. 1995. Species Diversity in Space and Time. Cambridge University Press.
  9. Hebert P.D., Cywinska A., Ball S.L., deWaard J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270(1512): 313-21.
  10. Hebert P.D.N, Stoeckle M.Y, Zemlak T.S, Francis C.M. Identification of birds through DNA barcodes. PLoS Biol. 2004;2:1657-1663
  11. Hollingsworth P.M. et al (2009). A DNA barcode for land plants. Proc Natl Acad Sci USA 106(31): 12794-7.
  12. Li M, Wunder J, Bissoli G, Scarponi E, Gazzani S et al. (2008) Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species. Cladistics 24: 727-745.
  13. IllergÄrd K, Ardell DH, Elofsson A. Structure is three to ten times more conserved than sequence-a study of structural response in protein cores. Proteins. 2009; 77:499-508.

Publication Details

Published in : Volume 1 | Issue 4 | July-August - 2015
Date of Publication Print ISSN Online ISSN
2015-08-25 2395-1990 2394-4099
Page(s) Manuscript Number   Publisher
347-352 IJSRSET151475   Technoscience Academy

Cite This Article

Irving Estevez, Stephen Mensah, Rujin Tian, Martin Fein, "DNA Barcoding and Phylogenetic Analysis of Plant Species: Urban Barcode Project of New York City", International Journal of Scientific Research in Science, Engineering and Technology(IJSRSET), Print ISSN : 2395-1990, Online ISSN : 2394-4099, Volume 1, Issue 4, pp.347-352, July-August-2015.
URL : http://ijsrset.com/IJSRSET151475.php

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