The Information Systems for DNA Barcode Data

Abstract

DNA barcoding is a novel concept for the taxonomic identification, in that it uses a specific short genetic marker in an organism’s DNA to discriminate species. In 2003, professor Paul D. N. Hebert, “the father of DNA barcoding”, of the University of Guelph, Ontario, Canada first proposed the idea to identify biological species using DNA barcode, where the mitochondrial gene cytochrome c oxidase subunit I (COI) was supposed to be the first candidate for animals (Hebert et al. 2003a). Their studies of COI profiling in both higher taxonomic categories and species-level assignment demonstrated that COI gene has significant resolutions across the animal kingdom except the phylum Cnidaria (Hebert et al. 2003b, Ward et al. 2005, Hajibabaei et al. 2006). From then on, a wide broad of taxonomic groups (i.e. birds, fish, butterflies, spiders, ants, etc) were examined by COI gene for its usability as the barcode (i.e. Hebert et al. 2004a, Hebert et al. 2004b, Greenstone et al. 2005, Smith et al. 2005, Barber and Boyce 2006, Meier et al. 2006, Kerr et al. 2007, Kumar et al. 2007, Pfenninger et al. 2007, Stahls and Savolainen 2008, Zhou et al. 2009). Meanwhile, other candidate genes, including Internal Transcribed Spacer (ITS), trnH-psbA intergenic spacer (trnH-psbA), Ribulose-bisphosphate carboxylase (rbcL) and Maturase K (matK) were analysed by different research groups (Jaklitsch et al. 2006, Evans et al. 2007, Ran et al. 2010, de Groot et al. 2011, Liu et al. 2011, Piredda et al. 2011, Yesson et al. 2011). Till recently, there are about 30 DNA barcode candidates are tested, and 4 to 8 of them are widely used for the identification of diversified taxonomic groups with a relatively good resolution. It has been estimated that there are 10 to 100 million species of living creatures in the earth, while what we know is very limited. Knowing the biodiversity is one of the crucial biological issues of ecology, evolutionary biology, bio-security, agro-biotechnology, bioresources and many other areas. For very long period, taxonomists have provided a nomenclatural hierarchy and key prerequisites for the society. However, the needs for species identification requested by non-taxonomists require the knowledge held by taxonomists. Therefore, a standardized, rapid and inexpensive species identification approach is needed to establish for the non-specialists. There had some attempts on the molecular identification systems based on polymerase chain reaction (PCR), especially in bacterial studies (Woese 1996, Zhou et al. 1997, Maiden et al. 1998, Wirth et al. 2006), but no successful solutions for broader scopes of eukaryotes (reviewed in Frezal and Leblois 2008). The DNA Barcode of Life project is another attempt to create a universal eukaryotic identification system based on molecular approaches. Following studies by Hebert et al.