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Biology LibreTexts

19.1.9: Barcoding

Barcoding is the term applied to a technology that is being developed to speed the identification of specimens of living things. So far, identification and classification of animals has progressed furthest.

Although each individual in most species has a unique genome sequence, the differences between individuals of one species are much smaller than the differences between individuals of different species. Thus determining the genome sequence of a specimen should enable it to be positively classified if the sequences of other members of its species are already in a database.

However, sequencing entire genomes of animals is an enormous undertaking. (Most mammals have some 3 billion base pairs of DNA.) A more practical approach is to settle on the sequence of a single gene that is found in all animal life.

The one that has been chosen for animals is the gene, COI, encoding the largest subunit of cytochrome c oxidase.


  • It is a mitochondrial gene and thus each cell has hundreds-to-thousands of copies of it as opposed to only two copies of each of its nuclear genes.
  • It has no introns (in animals).
  • Thanks to the redundancy of the genetic code, it can mutate quite freely, especially in the third position of its codons.
  • Furthermore mitochondrial gene sequences vary more between related species than their nuclear genes do. For example, while the sequence differences between the nuclear genes of humans and chimpanzee is only about 1%, the difference between their mitochondrial gene sequences is some 9%.
  • Within a species, however, there is little variation from specimen to specimen in their mitochondrial gene sequences.


  • The mitochondrial DNA is extracted.
  • A fragment from the 5' end of COI (~648 base pairs) is isolated (the entire gene has ~1500 base pairs).
  • The fragment is amplified by PCR using readily-available primers.
  • The sequence is determined and compared with those already in a database.

Early Results

Barcoding analysis of several hundred different birds has shown that barcode results usually reflect the species identification based on more conventional criteria. However, a few cases have arisen where:

  • specimens thought to belong to the same species differ substantially in the COI sequence and thus probably represent convergent evolution.
  • specimens thought to belong to different species have similar COI sequences and thus are probably local variants of what is actually a single species.

Looking Ahead

  • Development of appropriate barcoding genes for plants (whose COI genes vary little) and fungi (whose COI genes are interrupted by introns). One promising candidate for plants is the chloroplast gene rbcL which encodes the large subunit of RUBISCO.
  • Development of hand-held sequencers that can barcode the DNA of a specimen in the field.

Promoting the development of barcoding is The Consortium for the Barcode of Life (CBOL). Their home page (link below) provides other links describing goals, methods, achievements, etc. As of this writing, barcodes for over 112,000 species have been entered in databases.