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

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.