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DNA Barcoding of Plant Specimens at Huntsville Botanical Garden


Overview

As part of the HudsonAlpha Biotech Academy, high school students from the Madison County area have partnered with the Huntsville Botanical Garden to collect plant samples from native Alabama species and sequence their DNA to create a genetic barcode for each plant.  This DNA barcode can be included in an international database and used to identify the plant as well as compare it to other species.

Background

HudsonAlpha Biotech Academy

The HudsonAlpha Biotech Academy is an intensive, four-week active learning experience designed to provide a strong foundation in research lab skills as well as an introduction to the latest discoveries in genetics, genomics and biotechnology. The students learn basic molecular biology techniques, discover how to identify plant and animal species based on their DNA sequence, study the concepts of genetic engineering by producing and purifying red fluorescent protein and delve into the emerging field of synthetic biology. Additionally, Academy participants visit many research labs and associate companies at the HudsonAlpha Institute to explore the various careers and professions available in the field of biotechnology, exposing them to world-class scientists and cutting-edge technology.  Attendees are rising juniors or seniors that have been nominated by their school life science teachers. One student from each high school in the Madison County, Madison City and Huntsville City systems is invited to attend.

Beginning in 2013 with the first class of Biotech Academy, the Huntsville Botanical Garden has opened it gates to these students, allowing them to tour the Garden and learn about its conservation efforts for native Alabama plants.  Under the direction of Garden experts, the students have collected tissue samples from identified plants and learned the lab techniques necessary to generate a genetic DNA barcode for each species.

DNA Barcoding

The genetic sequence of an organism, or its DNA, can provide a highly specific tool to be used to identify that organism – at any life stage and in many different environments.  While the vast majority of the DNA sequence for any two plants is very similar, there are some regions where the code of molecules will be unique to a genus and often to a species.  By extracting a plant or animal’s DNA, sequencing the precise order of the chemical molecules and comparing that code to a database, we can often identify an organism down to the genus and species level.  This technique can be particularly valuable if we only have a small portion of a plant or an expert is not available to make an identification based on the plant’s morphology.

Researchers around the world contribute to this work through the International Barcode of Life project. The goal of the project is to use a short section of DNA from a standardized region of the genome of plants and animals to identify them – similar to how a barcode on a product in the grocery store allows it to be identified by a scanner. There are small changes in the DNA sequence of this standardized region that are unique to each species, allowing identification of a plant or animal from the DNA alone. The barcode sequences are maintained in a reference library of DNA that can be used to identify unknown specimens.

A fundamental aspect of this effort is the creation of a database populated with the genetic sequences or barcodes from a wide variety of species.  The collaboration between the Huntsville Botanical Garden and HudsonAlpha will provide valuable contributions to this effort.  The expert identifications of Garden specimens allow for direct submission and inclusion in the international databases that provide sequence and identity information to researchers.  Students in Biotech Academy collect samples from the Garden’s curated collections, with special emphasis on native Alabama specimens.  In the lab at HudsonAlpha, the students extract the plant’s DNA and analyze the sequences before submitting the information to the Barcode of Life database.  Each plant sequence contributes to the scientific community and documents information that can be used by research efforts around the world.

A DNA barcode of a plant consists of ~600 bases of DNA from the rbcL gene in the chloroplast. This region is highly conserved, meaning that it is so important for plant survival that it is present in all plants and has changed very little over time.  However, small regions of the gene do vary between different genus and species and by analyzing the differences in these areas the plant’s identify can be determined. A DNA barcode is not a complete sequence of a plant’s genome, which is many, many times larger than the short barcode region.  For example, the Loblolly pine genome is over 20 billion bases long.  Sequencing only the very short barcode region does not provide as much information about a plant as its full genome, but is considerably less expensive.

Current Status

Biotech Academy students have collected samples approximately 25 different specimens at the Huntsville Botanical Garden, some of them on several different occasions.  Each of the plant samples was processed by a student and sent out for sequencing.  In most cases, but not all, the sequencing test was successful and data was obtained that can be further reviewed and submitted to the Barcode of Life Database (BOLD) for possible inclusion.  Along with the DNA sequence of the plant, BOLD requires additional data such as photographs and GPS coordinates.  Attempts were made to collect this data during each Garden visit, but some additional high-quality pictures are still needed.

Due to the intensive schedule of activities during the Biotech Academy, the students are only able to do an initial scan of the sequence data and identify confirmation. Some of the plants are not currently included in the databases. Since each of these samples has been positively identified by an expert at the Garden, the sequence and additional plant information can result in a new and unique record in the database.  For example, Clematis morefieldii, a uniquely native Alabama plant, was accepted into the National Center for Biotechnology Information’s (NCBI) genetic information database in 2014. (Link to news release here and database record here.) Work is underway to process more of these samples and have them included in NCBI as well as the BOLD databases. Undergraduate students from the University of Alabama in Huntsville also contributed to this work during the spring semester of 2017 in a lab skills and research class taught at HudsonAlpha.

Future Work

The hope is to continue this work with the Garden and increase the number of plant sequences that are submitted to BOLD and NCBI.  While the work is slow, students benefit greatly from this project because they are able to participate in the process from beginning to end – collecting the samples in the field, processing the samples in the lab and computationally analyzing the resulting data.  A successful conclusion results in a contribution to science that is attributed to the students who did the work and recognizes the Huntsville Botanical Garden as the source of the sample.

Michele C. Morris
Workforce Development Lead
Educational Outreach

HudsonAlpha Institute for Biotechnology
601 Genome Way, Huntsville, AL 35806
256-327-0576
mmorris@hudsonalpha.org
hudsonalpha.org/education


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