When I say “barcode”, most of you will think about the 11-digit barcode on the product of market shelf and by scanning it, all the information details of the product can be accessed. But when “barcode” is together with “DNA”, what’s that mean?
DNA barcoding is a taxonomic technique that uses a short genetic marker from a standard and agreed-upon position in an organism’s genome to indentify it as belonging to a particular species. DNA barcode sequencesare very short relative to the entire genome and they can be obtained reasonably quickly and cheaply. The goal of it is to identify an unknown sample in terms of a known classification. DNA barcodes vary among individuals of the same species, but only to a very minor degree. If the DNA barcode region is effective, the minor variation within species will be much smaller than the differences among species.
Most eukaryote cells contain mitochondria, and mitochondrial DNA (mtDNA) has a relatively fast mutation rate. As the results, the variation in mtDNA sequences between species is significant, and, in principle, within species it is comparatively small. So, a 658-bp region at the 5’-end of the mitochondrial cytochrome C oxidase subunit I (COI) gene was proposed as a potential 'barcode',
The applications of DNA barcoding include, identifying plant leaves even when flowers or fruit are not available, identifying insect larvae, identifying the diet of an animal based on stomach contents or faeces, and identifying products in commerce. And if you have the effective DNA barcoding equipment, you can save some money at sushi bar by indentifying that the expensive “white tuna” is actually cheap “Mozambique Tilapia”as two students of New York City high school did.
Dr. ZHANG Ya-Ping’s research group (Kunming Institute of Zoology, the CAS) has applied DNA barcoding in indentifying amphibian species. Their “cold code” program about the worldwide amphibian maker gene screening, technical system construction and standard dataset refinement also has been proposed in the Fourth International Barcode of Life Conference.
Amphibians are special. Especially the species represent transition of aquatic creatures to land animals. Because of their extreme sensitivities to environment, they are behaving as the indicating species in the study of environmental and climatic changes. China’s amphibian fauna is comprised of at least 375 species of which nearly two-thirds are endemic. Unfortunately, 96 (26%) of these species are facing possible extinction (IUCN). DNA barcoding could provide a snapshot glimpse of genetic diversity of the largest number of threatened Asian amphibians, i.e. those that occur in China. But now, according to the updated research, the nucleotide sequences at the COI priming sites will lead to problems in the use of universal primers in amphibian barcoding. So, the challenge is to identify a method that facilitates the universal use of COI as the barcoding fragment to elucidate global patterns of diversity and outline priority areas and hotspots for conservation.
Recently, given this challenge, Dr. CHE Jing and her colleagues (KIZ, the CAS) selected representative Chinese amphibians from all three orders of amphibians to test the efficacy of two newly designed primers for amplifying and sequencing COI. In this study, 82 species (111 samples in total), crossing 12 families and 36 representative genera, whose identity was certain were selected to represent the diversity of Chinese frogs, salamanders and caecilians. The newly designed primers barcoded all sampled species, which includes caecilians, salamanders and frogs. And the single mitochondrial DNA barcode, which varied from 565 to 602 bp, correctly identified all individuals. The results suggest that the new primer pairs could universally amplify COI for the vast majority species of amphibians.
This research has enriched our knowledge of DNA barcoding dataset of amphibian, which compared to other vertebrates, such as fish, birds and arctic wildlives, is already way behind. The main findings of this study have published on Molecular Ecology Resources, (doi: 10.1111/j.1755-0998.2011.03090.x).
