Metabarcoding

Metabarcoding refers to the gene bank systems that seek to collect and make available to specialists from around the world through the Internet, the information contained in the DNA of all known taxa. For this, DNA of a short and standardized sequence is collected and used, one per taxon. The idea originated in 2003, at the suggestion of researchers from the University of Guelph, in the province of Ontario, Canada.[1]

Characteristics

The method requires each collected DNA to be archived with its corresponding "type specimen" (one for each taxon), in addition to the usual collection data. These types are stored in specific institutions (museums, molecular laboratories, universities, zoological gardens, botanical gardens, herbaria, etc.) one for each country, and in some cases, the same institution is assigned to contain the types of more than a country, in cases where some nations do not have the technology or financial resources to do so.

In this way, the creation of type specimens of genetic codes represents a methodology parallel to that carried out by traditional taxonomy.

In a first stage, the region of the DNA that would be used to make the barcode was defined. It had to be short and achieve a high percentage of unique sequences. For animals, algae and fungi, a portion of a mitochondrial gene which codes for subunit 1 of the cytochrome oxidase enzyme, CO1, has provided high percentages (95%), a region around 648 base pairs.[2]

In the case of plants, the use of CO1 has not been effective since they have low levels of variability in that region, in addition to the difficulties that are produced by the frequent effects of polyploidy, introgression, and hybridization, so the chloroplast genome seems more suitable .[3][4]

The construction of the genetic barcode library was initially focused on fish [5] and the birds,[6][7][8] which were followed by butterflies and other invertebrates.[9] In the case of birds, the DNA sample is usually obtained from the chest.

Researchers have already developed specific catalogs for large animal groups, such as bees, birds, mammals or fish. Another use is to analyze the complete zoocenosis of a given geographic area, such as the "Polar Life Bar Code" project that aims to collect the genetic traits of all organisms that live in polar regions; both poles of the Earth. Related to this form is the coding of all the ichthyofauna of a hydrographic basin, for example the one that began to develop in the Rio São Francisco, in the northeast of Brazil.[10][11]

The potential of the use of Barcodes is very wide, since the discovery of numerous cryptic species (it has already yielded numerous positive results),[12] the use in the identification of species at any stage of their life, the secure identification in cases of protected species that are illegally trafficked, etc.[13][14]

Projects

International search projects for "barcodes" are :

“Barcode of Life Database” o Barcoding of Life (BOLD).

This project belongs to the Canadian University of Guelph.

“Consortium for the Barcode of Life (CBOL)

This project was formed in May 2004.

“The International Nucleotide Sequence Database Collaborative”

This is a partnership between various institutions:

Controversies

Its detractors point out that, in relation to the high budgets they demand, its usefulness is not so high, taking into account the low reliability that identification through a single genetic expression offers, since some sequences do not provide information that adequately differentiates a single gene taxon of the others, although the objective is that the genetic code is a taxonomic complement for a greater efficiency of descriptions and integrative identifications.

See also


References
  1. Hebert P., A. Cywinska , S. Ball and J. deWaard (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B, Biological Sciences. 270:313-321.
  2. Stoeckle, M. Y. & Hebert, P. D. (2008). El código de barras de la vida. Investigación y ciencia, (387), 42-47.
  3. Newmaster S. G. et al. (2007). Testing candidate plant barcode regions in Myristicaceae. Molecular Ecology Notes. 1-11.
  4. Jaén-Molina, R., Caujapé-Castells, J., Fernández-Palacios, O., de Paz, J. P., Febles, R., Bramwell, D., ... & Khalik, K. A. Filogenia molecular de las Matthioleae Macaronésicas según la información de la región ITS.
  5. Cázarez Carrillo, D. E. Descripción de la larva de ‘‘Eucinostomus jonesii’’ (Pisces, Gerreidae) by morphological and genetic methods.
  6. Kerr, K. C., Lijtmaer, D. A., Barreira, A. S., Hebert, P. D., & Tubaro, P. L. (2009). Probing evolutionary patterns in Neotropical birds through DNA barcodes. PLoS One, 4(2), e4379.
  7. Lijtmaer, D. A., Kerr, K. C., Barreira, A. S., Hebert, P. D., & Tubaro, P. L. (2011). DNA barcode libraries provide insight into continental patterns of avian diversification. PloS one, 6(7), e20744.
  8. Lijtmaer, D. A., Kerr, K. C., Stoeckle, M. Y., & Tubaro, P. L. (2012). DNA barcoding birds: from field collection to data analysis. In DNA Barcodes (pp. 127-152). Humana Press.
  9. García Morales, A. E. (2013). Código de barras y análisis filogeográfico de rotíferos (Monogononta, Ploima) del sureste mexicano.
  10. de Carvalho, Daniel Cardoso; Cecília Gontijo Leal; Paulo dos Santos Pompeu; José Vanderval Melo Junior & Denise A. A. de Oliveira (2011). Aplicações da técnica de identificação genética - DNA Barcode - nos peixes da bacia do rio São Francisco. Boletim Sociedade Brasileira de Ictiología N°104. Departamento de Morfologia, Instituto de Biociências, Botucatu, São Paulo, Brasil.
  11. de Carvalho, Daniel Cardoso; Paulo dos Santos Pompeu; Cecília Gontijo Leal; Denise A. A. de Oliveira & Hanner, R. (2011). Deep barcode divergence in Brazilian freshwater fishes: The case of the São Francisco River Basin. Mitochondrial DNA, 2011.
  12. Hernández, Esmeralda Salgado (2008). El código de barras genético (“DNA barcoding”) como herramienta en la identificación de especies. Herreriana. Revista de divulgación de la ciencia. Vol. 4 (1).
  13. Hebert P. and G. Ryan (2005). The promise of DNA Barcoding for Taxonomy. Systematic Biology. 54(5):852-859.
  14. Hollingsworth, P. (2007). DNA barcoding: potential users. Genomics, Society and Policy. 3(2):44-47.
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