page_title: DNA barcoding
section_title: DNA extraction, amplification and sequencing
hierarchical_section_title: DNA barcoding / Methodology / DNA extraction, amplification and sequencing
caption_attribution_description: English: HiSeq sequencers at the facility of SciLifeLab in Uppsala, Sweden. Picture taken during excursion of SLU course PNS0169 in March 2019.
context_page_description: 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, an individual sequence can be used to uniquely identify an organism to species, in the same way that 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 c oxidase I gene, found in mitochondrial DNA. Other genes suitable for DNA barcoding are the internal transcribed spacer rRNA often used for fungi and RuBisCO used for plants. Microorganisms are detected using different gene regions.
context_section_description: DNA barcoding requires that DNA in the sample is extracted. Several different DNA extraction methods exist, and factors like cost, time, sample type and yield affect the selection of the optimal method.
  When DNA from organismal or eDNA samples is amplified using polymerase chain reaction (PCR), the reaction can be affected negatively by inhibitor molecules contained in the sample. Removal of these inhibitors is crucial to ensure that high quality DNA is available for subsequent analyzing.
  Amplification of the extracted DNA is a required step in DNA barcoding. Typically, only a small fragment of the total DNA material is sequenced (typically 400–800 base pairs) to obtain the DNA barcode. Amplification of eDNA material is usually focused on smaller fragment sizes (<200 base pairs), as eDNA is more likely to be fragmented than DNA material from other sources. However, some studies argue that there is no relationship between amplicon size and detection rate of eDNA.
  When the DNA barcode marker region has been amplified, the next step is to sequence the marker region using DNA sequencing methods. Many different sequencing platforms are available, and technical development is proceeding rapidly.
caption: HiSeq sequencers at SciLIfeLab in Uppsala, Sweden. The photo was taken during the excursion of SLU course PNS0169 in March 2019.
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