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DNA BARCODING, NCBI DATA TOOL AND MEGA AS A TEACHING AND RESEARCH TOOL FOR UNDERGRADUATE BIOLOGY LABORATORY ACTIVITIES

Abstract

In 2012, a project involving plant DNA barcoding was started at Gordon State College to improve student engagement in upper division and senior level research courses. DNA barcoding involves the collection of specimens for identification and the laboratory analysis of DNA barcode sequences. The data is then placed in a database for subsequent analysis. The National Center for Biotechnology (NCBI) houses a series of DNA sequence databases in GenBank. Additionally, Molecular Evolutionary Genetics Analysis (MEGA) is a freely available computer program that conducts statistical analysis of molecular evolution and aids in the construction of phylogenetic trees. This provides an excellent molecular tool to train students to collect, manage/analyze DNA barcode data, and compare it with GenBank DNA databases to construct phylogenetic trees. In fall 2012, 2014, 2016, and spring 2013 the Biotechnology and special research topics classes isolated genomic DNA from 30 vegetables and 30 fruit species taken from local grocery stores and nine plant species from the Gordon State College walking trail. Genomic DNA preparation was done using PureLink TM plant DNA Total DNA Purification Kits (Invitrogen, Carslbad, Ca). The students amplified chloroplast RuBisCO large subunit (rbcl) sequences by using a polymerase chain reaction (PCR). The isolated genomic DNA templates and DNA sequencing was created by using MEGA software to understand the evolutionary relationship of the chosen species and to further analyze the DNA barcoding data. This provides an excellent educational research project within the undergraduate upper division biology lab classes and special research topics course.

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