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Identification of Unknown Organisms by DNA Barcoding: A Molecular Method for Species Classification

Project ID: 45
Principal Investigator: Jacque Keele
Research Topic: Invasive Species
Priority Area Assignments: 2014 (Zebra and Quagga Mussels)
Funded Fiscal Years: 2014
Keywords: dna barcoding, species identification, classification, monitoring

Research Question

Over the last ten years, DNA barcoding has enabled researchers to change how species identification is performed. DNA barcoding involves isolating DNA from the organism of interest, performing polymerase chain reaction (PCR) of the cytochrome oxidase 1 (CO1) gene, sequencing the PCR product, and identifying the organism by comparing the sequence to a database of over 2 million CO1 gene sequences. This project sets out to determine the effectiveness of utilizing DNA barcoding as a more cost effective way to identify species that are of concern to Reclamation, other than using traditional taxonomic identification which can be costly and time consuming. The goal of this research is to optimize the DNA barcoding process so that individual specimens collected in the field can be identified to the species level. Reclamation can use this DNA identification tool to identify invasive species and various phyla for biodiversity studies. The effectiveness of DNA barcoding will be tested on invasive species that pose a threat to Reclamation, and also a variety of other plants, insects, mammals, and birds currently studied by Reclamation.

Need and Benefit

The Consortium for the Barcode of Life (COBL) organizes gene sequences into a database (BOLD) for validation. An unknown sequence can be entered into the database and compared to all verified sequences. In 2011, the U.S. Food and Drug Administration (FDA) approved DNA barcoding for use in fish identification for human consumption. Over 170,000 species of plants and animals have been recorded, with over two million specimens verified with barcoding.
Mitochondria were selected as a target for barcoding because its genome is highly conserved along the maternal lineage. Mitochondria have a fast mutation rate, resulting in detectable variations between species, allowing scientists to identify an organism based on mitochondrial sequences. The cytochrome oxidase 1 (CO1) of the mitochondrial genome was chosen as the standardized region of the genome for universal use in species identification. A small section (~700 base pairs) was chosen because it was small enough to be sequenced cheaply and quickly, but long enough to identify the species.
While all species have the CO1 region of the mitochondrial genome, plant species evolve too slowly to have changes in the CO1 gene, so two regions in the chloroplast are traditionally used. COBL has adapted their DNA barcoding to include a variety of tests for most phyla all of which are published by COBL. Reclamation biologists would greatly benefit from DNA barcoding as it significantly reduces the cost and effort typically associated with multi species identifications. Some applications include: analyzing a leaf when no fruit or flower is present; identifying fish larvae; identifying insect adults and larvae; identifying birds, and identifying the diet of an animal. Reclamation has already had success identifying fish using the DNA barcoding method.
DNA barcoding will be beneficial to Reclamation for early detection of new invasive species. Being able to correctly and quickly identify an organism is important, because it enables mangers to make water management decisions based on the pest. Traditional taxonomy involves skilled taxonomists and sometimes requires specialized preservation methods that are toxic (i.e. formalin). Samples collected for DNA barcoding analysis require a small amount of tissue from the organism to be preserved in alcohol. The results can be obtained in less than two weeks. Once Reclamation has determined the efficacy of DNA barcoding, samples from across the United States can be sent to Reclamation for cost effective species identification.

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Research Products

Bureau of Reclamation Review

The following documents were reviewed by experts in fields relating to this project's study and findings. The results were determined to be achieved using valid means.

Identification of Unknown Organisms by DNA Barcoding: A Molecular Method for Species Classification (final, PDF, 859KB)
By Jacque Keele
Report completed on December 12, 2014

DNA barcoding is a molecular method for species identification. The goal of this research was to identify ways that researchers at Reclamation can use this technique to enhance their research. This report includes a literature review of DNA barcoding methods, a summary of some of the barcoding projects performed, and a summary of the lessons learned from the DNA barcoding research done this year. A variety of organisms (birds, fish, mammals, invertebrates) were analyzed this year with varying de
Keywords: polymerase chain reaction, dna barcoding, species identification, dna analysis

This information was last updated on December 20, 2014
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