Kept on Wikipedia:Metabarcoding
Metabarcoding is the barcoding of DNA/RNA in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between the barcoding and metabarcoding is that metabarcoding does not focus on one specific organism, but instead aims to determine species composition within a sample.
The metabarcoding procedure, like general barcoding, proceeds in order through stages of DNA extraction, PCR amplification, sequencing and data analysis. A barcode consists of a short variable gene region (for example, see different markers/barcodes) which is useful for taxonomic assignment flanked by highly conserved gene regions which can be used for primer design.[1] Different genes are used depending if the aim is to barcode single species or metabarcoding several species. In the latter case, a more universal gene is used. Metabarcoding does not use single species DNA/RNA as a starting point, but DNA/RNA from several different organisms derived from one environmental or bulk sample.
The idea originated in 2003, at the suggestion of researchers from the University of Guelph, in the province of Ontario, Canada.[2]
Method
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.[3]
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 .[4][5]
Applications
The construction of the genetic barcode library was initially focused on fish [6] and the birds,[7][8][9] which were followed by butterflies and other invertebrates.[10] 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.[11][12]
The potential of the use of Barcodes is very wide, since the discovery of numerous cryptic species (it has already yielded numerous positive results),[13] 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.[14][15]
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
- Barcode of Life Data System (BOLD)
- Consortium for the Barcode of Life (CBOL)
- International Nucleotide Sequence Database Collaboration (INSDC)
- Molecular marker
- Taxonomic impediment
References
- ↑ Pierre, Taberlet (2018-02-02). Environmental DNA : for biodiversity research and monitoring. Bonin, Aurelie, 1979-. Oxford. ISBN 9780191079993. OCLC 1021883023. Search this book on
- ↑ 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.
- ↑ Stoeckle, M. Y. & Hebert, P. D. (2008). El código de barras de la vida. Investigación y ciencia, (387), 42-47.
- ↑ Newmaster S. G. et al. (2007). Testing candidate plant barcode regions in Myristicaceae. Molecular Ecology Notes. 1-11.
- ↑ 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.
- ↑ Cázarez Carrillo, D. E. Descripción de la larva de ‘‘Eucinostomus jonesii’’ (Pisces, Gerreidae) by morphological and genetic methods.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ García Morales, A. E. (2013). Código de barras y análisis filogeográfico de rotíferos (Monogononta, Ploima) del sureste mexicano.
- ↑ 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.
- ↑ 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.
- ↑ 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).
- ↑ Hebert P. and G. Ryan (2005). The promise of DNA Barcoding for Taxonomy. Systematic Biology. 54(5):852-859.
- ↑ Hollingsworth, P. (2007). DNA barcoding: potential users. Genomics, Society and Policy. 3(2):44-47.
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