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

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.

Authors and Affiliations

Irving Estevez
Biology Undergraduate, LSAMP Scholar, City College of New York
Stephen Mensah
Biology Undergraduate, Bronx Community College, City University of New York
Rujin Tian
PhD, Associate Professor, Department of Biological Science, Bronx Community College, City University of New York
Martin Fein
PhD, Chairperson Professor, Department of Biological Science, Bronx Community College, City University of New York

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

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Publication Details

Published in : Volume 1 | Issue 4 | July-August 2015
Date of Publication : 2015-08-25
License:  This work is licensed under a Creative Commons Attribution 4.0 International License.
Page(s) : 347-352
Manuscript Number : IJSRSET151475
Publisher : Technoscience Academy

Print ISSN : 2395-1990, Online ISSN : 2394-4099

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.
Journal URL : http://ijsrset.com/IJSRSET151475

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