DNA barcoding

DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that, by comparison with a reference library of such DNA sections (also called 'sequences'), an individual sequence can be used to uniquely identify an organism to species, in the same way as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database. These 'barcodes' are sometimes used in an effort to identify unknown species, parts of an organism, or simply to catalog as many taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries. DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that, by comparison with a reference library of such DNA sections (also called 'sequences'), an individual sequence can be used to uniquely identify an organism to species, in the same way as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database. These 'barcodes' are sometimes used in an effort to identify unknown species, parts of an organism, or simply to catalog as many taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries. Different gene regions are used to identify the different organismal groups using barcoding. The most commonly used barcode region for animals and some protists is a portion of the cytochrome oxidase I (COI or COX1) gene, found in mitochondrial DNA. Other genes suitable for DNA barcoding are the Internal transcribed spacer (ITS) rRNA often used for fungi and RuBisCO used for plants. Microorganisms are detected using different gene regions. The 16S rRNA gene for example is widely used in identification of prokaryotes, whereas the 18S rRNA gene is mostly used for detecting microbial eukaryotes. These gene regions are chosen because they have less intraspecific (within species) variation than interspecific (between species) variation, which is known as the 'Barcoding Gap'. Some applications of DNA barcoding include: identifying plant leaves even when flowers or fruits are not available; identifying pollen collected on the bodies of pollinating animals; identifying insect larvae which may have fewer diagnostic characters than adults; or investigating the diet of an animal based on its stomach content, saliva or feces. When barcoding is used to identify organisms from a sample containing DNA from more than one organism, the term DNA metabarcoding is used, e.g. DNA metabarcoding of diatom communities in rivers and streams, which is used to assess water quality. DNA barcoding techniques were developed from early DNA sequencing work on microbial communities using the 5S rRNA gene. In 2003, specific methods and terminology of modern DNA barcoding were proposed as a standardized method for identifying species, as well as potentially allocating unknown sequences to higher taxa such as orders and phyla, in a paper by Paul D.N. Hebert et al. from the University of Guelph, Ontario, Canada. Hebert and his colleagues demonstrated the utility of the cytochrome coxidase I (COI) gene, first utilized by Folmer et al. in 1994, using their published DNA primers as a tool for phylogenetic analyses at the species levels as a suitable discriminatory tool between metazoan invertebrates. The 'Folmer region' of the COI gene is commonly used for distinction between taxa based on its patterns of variation at the DNA level. The relative ease of retrieving the sequence, and variability mixed with conservation between species, are some of the benefits of COI. Calling the profiles 'barcodes', Hebert et al. envisaged the development of a COI database that could serve as the basis for a 'global bioidentification system'.