DNA Barcoding: A potential supplement to conventional taxonomy for species identification
Authors: Jameel Akhtar, A Kandan, Pardeep Kumar and Monika Malik
Plant Quarantine Division, ICAR- National Bureau of Plant Genetic Resources, New Delhi- 110012


After about 250 years of conventional science of biological diversity, systematic studies have distinguished identity and named only ~1.8 million species including ~69000 species of fungi and ~15000 nematodes. As many as 1.6 million species of fungi are thought to exist and a million of nematodes await discovery. This realizes that there is a stark issue of limited taxonomists engaged in different categories of organism identification. And, the current taxonomic system is heavily depended on taxonomists. Few taxonomists can reliably diagnose even 1,000 species and that means we need ~100,000 taxonomists to identify earth's existing species. This is a great taxonomic bottle-neck in biodiversity conservation. Perhaps, this is one of the obvious reasons in driving biologists/ taxonomists towards a new approach for rapid species identification called DNA sequence-based barcoding.

DNA is scaffold of a taxonomic reference system, which is different than the current practice and concept in unitary taxonomy where the type specimen serves as the central reference for comparisons (Tautz et al. 2003). DNA barcode is a unique pattern of DNA sequence that identifies each living thing, just as the unique pattern of bars in a universal product code (UPC) identifies each consumer product. The International Barcode of Life (iBOL) organizes collaborators from more than 150 countries to participate in a variety of "campaigns" to census diversity among plant and animal groups - including ants, bees, butterflies, fish, birds, mammals, fungi, and flowering plants plants - and within ecosystems - including the seas, poles, rain forests, kelp forests, and coral reefs.

Application of DNA Barcode

The success of this technology is very well supported by literature touching different areas related to biodiversity, like, species identification using reference barcode sequences, identification of taxa from cryptic species, conservation biology studies, molecular phylogenetics studies, identification of invasive plant species threats to global biodiversity, analysis for genetic distances between species through tree creation from differences in DNA barcodes, etc.

Identifying Species

The concept of DNA sequence-based barcode for species identification is now widely utilized using the standard DNA Barcodes, e.g. mitochondrial cytochrome oxidase I (COI or COXI) for animals, choloroplast ribulose-bisphosphate carboxylase gene (rbcL) and the maturase K gene (matK) for plants and nuclear ITS1 spacer and the ITS2 spacer region for fungi. The number for barcoded species is ~470,000 including animal species ~388,596 in Barcode of Life Data (BOLD) System. In addition, It has been contributing in resolution of cryptic species in neo-tropical, tropical and extra-tropical biodiversity. Astraptes fulgerator and Microgastrine wasps have a high number of cryptic species and morphology- based taxonomy alone was unable to resolve the problem. DNA barcoding resolved the issue and realized dramatic increases in species numbers from these cases.

Distinguishing invasive species

Biological invasion by exotic species is considered as one of the greatest threats to ecological biodiversity worldwide. Among invasive aliens, a number of plant species pose serious threat to water bodies. Many related species to the genera Myriophyllum, Ludwigia and Cabomba, are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is very difficult in a vegetative stage. Aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL, based on the criteria of universal application, high sequence divergence and level of species discrimination. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species.

Conserving biodiversity

Taxonomy is prerequisite to effectively describe and understand the worlds' biodiversity for their utilization and conservation. The earth is experiencing the rapid extinction of species. Daughety et al. (1990) ironically stated that what is not described cannot be protected on earth. Critical endangered species needs intervention prevent their extinction. DNA barcoding can enable us to identify species, hence identifying biodiversity rich areas, and design suitable conservation strategies.

Studying phylogenetics

DNA barcoding can be used as a starting point for phylogenetic and population genetics studies as it can provide only first signal of the extent and nature of population divergence. DNA barcodes do not have sufficient phylogenetic signal to resolve evolutionary process, whereas, phylogenetic analysis requires more sequence data from multiple loci even from different genomic compartments.

Issues with DNA Barcoding

About 2.3 million DNA barcodes representing ~300,000 species are now available on public databases and are now available to the researchers and would certainly be used as reference material. These may later pose some issues in future such as monitoring, reliability, reproducibility, validation and curation of data. Therefore, standard guideline is essential including comprehensive DNA sequence library, use of universal agreement on: region of the genome (housekeeping genes) to sequence; and taxonomic standard for governing those web-based links/ data base, and strong regional cooperation and funding for global network for easy access to users/researchers. Reliable applicability is another concern, where, some barcode markers e.g. rbcL trnH-psbA, matK, etc. do not amplify in some plant groups. Even the primers suggested for angiosperms failed to give amplification in Rosaceae and primers for the Pinaceae also failed to amplify in Cedrus sp. Keeping inconsistency of amplification product in view, the integration of multiple genes/ DNA barcodes with conventional taxonomy for improved accuracy in species identification is ideally fit.

Conclusion

Though DNA barcoding is having some serious issues like lack fixed threshold value for divergence, no universal gene region as 'barcode' optimized across kingdoms, sometimes primers suggested for specific group of organism fail to give amplification in others, there is no doubt about the potentiality of DNA barcoding as a global strategy/ tool which is, of course, supportive to scientists working in biodiversity research, especially, taxonomy for the purpose to identify diverse taxa. No single method of advancing science is so powerful in overcoming issues of species identification. Therefore, the concept of DNA sequence-based barcode would probably be the best supplement for conventional species identification accompanied by specimen-based digitized diagnostic features to overcome the issues of taxonomic crisis/ species identification.

References:

1. Daugherty CH, Cree A, Hay JM, Thompson MB. (1990). Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature, 347: 177-179.

2. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2003). A plea for DNA taxonomy. Trends in Ecology & Evolution 18: 70-74.


About Author / Additional Info:
I am currently working on plant disease diagnosis and seed-borne fungal/bacterial pathogens as Senior Scientist (Plant Pathology for the last five years) in Plant Quarantine Division of ICAR-NBPGR, New Delhi. I have also worked as an Assistant Professor in the Department of Plant Pathology, Birsa Agricultural University, Ranchi, Jharkhand, India for more than 6 years.