Abstract
DNA barcoding has evolved as an effective species identification tool in diverse areas such as phylogeny, ecology, population genetics, and biodiversity. In this approach, a short DNA sequence from a standardized locus is employed for species identification. The technique is simple, time and cost effective, and accurate. Selection of correct DNA marker is the main criterion for success in DNA barcoding. Compared to animals, DNA barcoding is more difficult in plants, as there are multiple consensuses about selection of barcoding markers for plants DNA barcoding. Some common plant barcoding markers are chloroplast genes such as matK, rbcL, ropC1, ropB, and trnL; chloroplast intergenic specers trnH-psbA, atpF-atpH, and pdbK-psbI; and the nuclear ribosomal internal transcribed spacer (ITS). These markers can be used alone or in combinations with other markers or spacers. In this chapter, the basic requirements, selection of markers, databases, advantages, and limitations of DNA barcoding have been discussed.
TopBarcoding Project Has Multiple Components
The Barcode of Life Database (http://www.barcodeoflife.org/) recognises four basic components involved in a barcoding project:
- 1.
Specimens: Specimen collection, storage still processing and proper description etc. are initial processes involved in a barcoding project. Stored identified specimens in museums, zoos, herbaria and seed bank etc. are the guidance source for description and identification of specimens.
- 2.
Analysis in Laboratory: Different barcoding protocols are necessary to obtain DNA barcode sequences from different specimens. The first task is to find an appropriate method of DNA isolation which is based on the type of the specimen to be processed. The second task is to select appropriate primers and PCR condition. This is followed by amplification of the region of interest and DNA sequencing. The process can be completed in few hours within a reasonable cost. One has to submit the sequence data obtained to a barcoding database for subsequent analysis.
- 3.
The Database: The most crucial component of the Barcoding project is a common platform of a public reference library which is a repository of identified barcodes. This database can be used as a guide to identify unknown specimens based on known specimen information. Currently two major barcode databases serve this purpose.
The International Nucleotide Sequence Database (INSD): This is a collaborative approach maintained for a very long time by three leading sequence database groups of world which are GenBank in the U.S., the European Molecular Biology Lab (EMBL) in Europe and the DNA Data Bank of Japan (DDBJ). They have collaboration with Barcoding initiative CBOL (The Consortium for the Barcode of Life) and accept the CBOL’s data standards for barcode records.