DNA Barcoding: Background, Procedure, Applications

Current Affairs Notes » DNA Barcoding

In News: The MIT team has developed a new retrieval technique to pull out the required file from the data repository. It involves encapsulating each DNA file into a small silica particle. Each capsule is labeled with single-stranded DNA “barcodes” that correspond to the contents of the file.

What is DNA Barcoding

DNA barcoding is a system for fast and accurate species identification that makes the ecological systems more accessible by using short DNA sequences instead of whole-genome and is used for eukaryotes. The short DNA sequence is generated from the standard region of the genome known as a marker. DNA barcoding has many applications in various fields like preserving natural resources, protecting endangered species, controlling agriculture pests, identifying disease vectors, monitoring water quality, authentication of natural health products, and identification of medicinal plants.

Background

The biological effects of global climate lead to the importance of the identification of organisms to preserve species because of increasing habitat destruction. About 5 to 50 million plants and animals are living on earth, out of which less than 2 million have been identified. The extinction of animals and plants is increasing yearly means thousand of them are lost each year and most of them are not identified yet. This destruction and endangerment of the ecosystem have led to an improved system for identifying species. In recent years new ecological approach called DNA barcoding has been proposed to identify species and ecology research.

DNA barcoding is a system for fast and accurate species identification which will make the ecological systems more accessible. It first came to the attention of the scientific community in 2003 when the science research group of Paul Hebert at the University of Guelph published a paper titled “biological identifications through DNA bar codes”. DNA barcoding is a new tool for the identification of species and for taxonomic research. It is not a new concept as Carl Woese used rRNA and molecular markers like rDNA and mtDNA to discover archaea i.e. prokaryotes and then for drawing an evolutionary tree.

How does it work

DNA barcoding uses a short DNA sequence instead of the whole genome and it is used for eukaryotes. The short DNA sequence is taken from the standard region of the genome to generate a DNA barcode. A DNA barcode is a short DNA sequence made of four nucleotide bases A (Adenine), T (Thymine), C (Cytosine), and G (Guanine). Each base is represented by a unique color in the DNA barcode. Even non-experts can identify species from small, damaged, or industrially processed material.

The standard region used to generate DNA barcodes is known as the marker. This marker is different in different species like COI or cox1 (Cytochrome C Oxidase 1) present in the mitochondrial gene in animals and recognized by the International Barcode of Life (IBOL) as an official marker for animals, because of its small intra-specific and large interspecific differences in animals. It is not suitable for other groups of organisms because it is uniform in them. So, ITS (Internal Transcribed Spacer) for fungus and two genes rbcl and matK, from the chloroplast genome are recognized as barcode markers for plants by IBOL.

The sequence data generated from standardized regions is used for the identification of organisms and to construct a phylogenetic tree. In this tree-related individuals are clustered together and can provide a large amount of information about specie.

The procedure of DNA Barcoding

The process of DNA barcoding involves two basic steps: The first step is to build a barcode library of identified species and the second is to match the barcode sequence of the unknown sample with the barcode library (known as sequence alignment) for its identification.

The first step requires ecologic expertise in selecting one or several individuals per species as reference samples in the barcode library. Tissue samples can be collected from live specie in the field or from specimens in museums for generating. These specimens go through lab processes that are tissue sampling and DNA processing and sequencing to generate DNA barcodes in form of the chromatogram. The chromatogram is a visual representation of a DNA sequence produced by the sequencer. This barcode can be stored in the database for future use or can be used as a query sequence to be compared with the sequence already present in the database. 

Applications

Controlling Agricultural Pest

DNA barcoding can help in identifying pests in any stage of life making it easier to control them saving farmers from the cost of billion dollars from pest damage. The global tephritid barcoding initiative contributes to the management of fruit flies by providing tools to identify and stop fruit flies at borders.

Identifying Disease Vectors

DNA barcoding allows non-ecologists to identify the vector species that can cause serious infectious diseases to animals and humans, to understand these diseases and cure them. A global mosquito barcoding initiative in building a reference barcode library that can help public health officials to control these diseases causing vector species more effectively and with very less use of insecticides.

Sustaining Natural Resources

Using DNA barcoding, natural resource managers can monitor the illegal trade of products made of natural resources like hardwood trees. Fishbol is a reference barcode library for hardwood trees to improve the management and conservation of natural resources.

Protecting Endangered Species

Primate Population is reduced in Africa by 90% because of bush meat hunting. DNA barcoding can be used by law enforcement on bush meat in local markets which is obtained from bush meat.

Monitoring Water Quality

Drinking water is a process resource for a living being. By studying organisms living in lakes, rivers, and streams, their health can be measured or determined. DNA barcoding is used to create a library of these species that can be difficult to identify. Barcoding can be used by environmental agencies to improve the determination of quality and to create better policies that can ensure a safe supply of drinking water.

Routine Authentication of Natural Health Products

The authenticity of natural health products is an important legal, economic, health, and conservation issue. Natural health products are often considered safe because of their natural origin.

Identifying plant leaves even if flowers or fruit are not available

Identification of medical plants

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