Aplicación de los códigos de barras de DNA en el descubrimiento de la diversidad animal marina.

Autores/as

  • Carlos Márquez

DOI:

https://doi.org/10.37543/oceanides.v30i2.150

Palabras clave:

DNA, código de barra, COI, diversidad animal, Montaña submarina

Resumen

Los códigos de barras de DNA constituyen un instrumento cuyo objetivo central es la identificación acertada de todas las especies existentes en planeta. La secuencia empleada como identificador de especies animales es un fragmento del gen mitocondrial Citocromo Oxidasa I (COI), cuya longitud es de 350 a 800 pb. El fragmento ha resultado útil en la identificación de especies crípticas y ha ampliado el conocimiento de la diversidad animal; no obstante, no resulta exitoso en plantas y hongos y es inconsistente en diversos grupos como las esponjas de mar. El gen COI es un recurso que a pesar de sus inexactitudes ha aportado enormes beneficios para el conocimiento de la biodiversidad. En este trabajo se analiza la información actual que está en la base de datos
BOLD Systems v3, se examina la dinámica de BOLD a través del tiempo y se complementa con información reciente de la literatura. Existen varios hechos que el análisis revela, entre ellos que la generación de secuencias es notable entre 2009 y 2013, y se aprecia una aceleración de 2013 a 2015. Existen datos contrastantes tales como que de las 52525 especies de moluscos marinos sólo se conozcan los códigos del 9.2% y de las 47217 especies de artrópodos se tengan códigos para el 7.6%, en contraste con las 21515 especies de cordados marinos que cuentan con los códigos para el 33.8%. Esta comparación indica un sesgo a favor de las especies carismáticas y de las que tienen importancia económica. Destaca que el número de secuencias de todas las formas de vida que están asociadas a una especie bien identificada siempre está relacionado a un 28 a 30% de especies interinas, ya que es difícil asignarles un nombre definitivo, lo que indica un alto nivel de incertidumbre.

Descargas

Los datos de descargas todavía no están disponibles.

Citas

Ardura, A., A.R. Linde, J.C. Moreira & E. GarcíaVazquez. 2010. DNA barcoding for conservation and management of Amazonian commercial fish. Biol. Conserv., 143: 1438-1443. https://doi.org/10.1016/j.biocon.2010.03.019

Arndt, A., C. Márquez, P. Lambert & M.J. Smith. 1996. Molecular phylogeny of Eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence. Mol. Phylogenet. Evol., 6: 425-437.

https://doi.org/10.1006/mpev.1996.0091

Arnot, D.E., C. Roper & R.A.L. Bayoumi. 1993. Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciporum circumsporozoite gene can genetically barcodes isolates. Mol. Biochem. Parasit., 61: 15-24.

https://doi.org/10.1016/0166-6851(93)90154-P

Ausubel, J.H., D.T. Crist & P.E. Waggoner (Eds.). 2010. First census of marine life 2010. Highlights of a decade of discovery. Publication of Census of Marine Life, Washington, D.C., 68p.

Avise, J.C. 1974. Systematic value of electrophoretic data. Syst. Zool., 23: 465-481. https://doi.org/10.1093/sysbio/23.4.465

Avise, J.C. 2004. Molecular Markers, Natural History, and Evolution. (Second Edition). Sinauer, Sunderland, MA. 684 p.

Ayala, F.J. & J.R. Powell. 1972. Allozymes as diagnostic characters of sibling species of Drosophila. P. Natl. Acad. Sci. U.S.A., 69: 1094-1096. https://doi.org/10.1073/pnas.69.5.1094

Baek, S., I. Ha, S. Kim, S.H. Lee, H.H. Oh, D.C. Moon, W. Kim & Y. Kim. 2013. Construction of an integrated barcode database for the molecular identification of species. BioChip J., 7(3):242-246. https://doi.org/10.1007/s13206-013-7307-4

BOLD Systems v3. 2015. http://www.boldsystems. org/.

Bucklin, A., D. Steinke & L. Blanco-Bercial. 2011. DNA barcoding of marine metazoa. Annu. Rev. Mar. Sci., 3: 471-508.

https://doi.org/10.1146/annurev-marine-120308-080950

Cantatore, P., M. Roberti, G. Rainaldi, M.N. Gadaleta & C. Saccone. 1989. The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus, J. Biol. Chem., 264:10965-10975.

https://doi.org/10.1016/S0021-9258(18)60413-2

CBOL Plant Working Group. 2009. A DNA barcode for land plants. P. Nat. Acad. Sci. U.S.A., 106: 12794-12797.

Census of Marine Life (CoML). 2015. http://www.coml.org/.

Chavan, V. & S. Krishnan. 2003. Natural history collections. A call for national information structure. Curr. Sci. INDIA, 84: 34-42.

Cognato, A.I. 2006. Standard percent DNA sequence difference for insects does not predict species boundaries. J. Econ. Entomol., 99: 1037-1045. https://doi.org/10.1093/jee/99.4.1037

Consortium for the Barcode of Life (CBOL). 2015. http://www.barcodeoflife.org/.

Cook, C.E., Q. Yue & M. Akam. 2005. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc. Biol. Sci., 272 (1569): 1295-1304. https://doi.org/10.1098/rspb.2004.3042

Costello, M.J., M. Coll, R. Danovaro, P. Halpin, H. Ojaveer & P. Miloslavich. 2010. A census of marine biodiversity knowledge, resources, and future challenges. PLos ONE, 5 (8): e12110. https://doi.org/10.1371/journal.pone.0012110

Delarbre, C., A.S. Rasmussen, U. Arnason & G. Gachelin. 2001. The complete mitochondrial genome of the hagfish Myxine glutinosa: unique features of the control region. J. Mol. Evol., 53:634-641. https://doi.org/10.1007/s002390010250

Dobzhansky, T. 1973. Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach., 35: 125-129.

https://doi.org/10.2307/4444260

Erpenbeck, D., J.N.A. Hooper & G. Wörheide. 2006. CO1 phylogenies in diploblasts and the "Barcoding of Life"- are we sequencing a suboptimal partition? Mol. Ecol. Notes, 6: 550-553. https://doi.org/10.1111/j.1471-8286.2005.01259.x

Ebach, MC. 2011. Taxonomy and the DNA barcoding enterprise. Zootaxa 2742: 67-68. https://doi.org/10.11646/zootaxa.2742.1.5

Elías-Gutiérrez, M. & M. Valdez-Moreno. 2008. A new cryptic species of Leberis Smirnov, 1989 (Crustacea, Cladocera, Chydoridae) from the mexican semi-desert region, highlighted by DNA barcoding. Hidrobiológica, 18 (1): 63-74.

Encyclopedia of Life (EOL). 2015. http://www.eol. org/.

Ferraris, J.D. & S.R. Palumbi (Eds.). 1996. Molecular Zoology: Advances, Strategies and Protocols. Wiley-Liss, 580 p.

Fish barcode of Life (FISH-BOL). 2015. http:// www.fishbol.org/.

Fitch, W.M. & E. Margoliash. 1967. Construction of phylogenetic trees. Science 155: 279-284. https://doi.org/10.1126/science.155.3760.279

Floyd, R., E. Abebe, A. Papert & M. Blaxter. 2002. Molecular barcodes for soil nematode identification. Mol. Ecol. 11: 839-850. https://doi.org/10.1046/j.1365-294X.2002.01485.x

Floyd, R., J. Lima, J. deWaard, L. Humble & R. Hanner. 2010. Common goals: policy implications of DNA barcoding as a protocol for identification of arthropod pests. Biol. Invasions., 12: 2947-2954. https://doi.org/10.1007/s10530-010-9709-8

Gai,Y., D. Song, H. Sun, Q. Yang & K. Zhou. 2008. The complete mitochondrial genome of Symphylella sp. (Myriapoda:Symphyla): Extensive gene order rearrangement and evidence in favor of Progoneata. Mol. Phylogenet. Evol., 49(2): 574-585. https://doi.org/10.1016/j.ympev.2008.08.010

Getta, R., L.G. Lohmmann,S. Magallón, D.P. Faith & 12 authors. 2014. Biodiversity only makes sense in the light of evolution. J. Biosci., 39: 333-337. https://doi.org/10.1007/s12038-014-9427-y

Global Biodiversity Information Facility (GBIF). 2015. http://www.gbif.org/.

Grande, C., J. Templado, J.L. Cervera & R. Zardoya. 2004. Phylogenetic relationships among Opisthobranchia (Mollusca:Gastropoda) based on mitochondrial cox 1, trnV, and rrnL genes. Mol. Phylogenet. Evol., 33: 378-388. https://doi.org/10.1016/j.ympev.2004.06.008

Hanner, R., S.Becker, N.V. Ivanova & D. Steinke. 2011. FISH-BOL and seafood Identification: Geographically dispersed case studies reveal systemic market substitution across Canada. Mitochondr. DNA, 22(S1): 106-122. https://doi.org/10.3109/19401736.2011.588217

Harris, H. 1966. Enzyme polymorphism in man. P. Roy. Soc. Lond. B.164: 298-310. https://doi.org/10.1098/rspb.1966.0032

Hebert, P.D.N., A. Cywinska, S.L. Ball & J.R. DeWaard. 2003a. Biological identification through DNA barcodes. P. Roy. Soc. B.270: 313-321. https://doi.org/10.1098/rspb.2002.2218

Hebert, P.D.N., S. Ratnasingham & J.R. DeWaard. 2003b. Barcoding animal life: cytochrome C oxidase subunit 1 divergences among closely related species. P. Roy. Soc. B. 270 (Suppl.): S96-99. https://doi.org/10.1098/rsbl.2003.0025

Hebert, P.D.N., E.H. Penton,J. Burns, D.H. Janzen & W. Hallwachs. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. P. Nat. Acad. Sci. U.S.A.,101: 14812-14817. https://doi.org/10.1073/pnas.0406166101

Hillis, D.M., C. Moritz & B.K.Mable. 1996. Molecular Systematics. Second Edition, Sinauer Associates, 655 p. https://doi.org/10.2307/1447682

International Barcode of Life Project (iBOL). 2015. http://www.ibol.org/.

Knudsen, B., A.B. Kohn, B. Nahir, C.S. McFadden & L.L. Moroz. 2006. Complete DNA sequence of the mitochondrial genome of the sea-slug: conservation of the gene order in Euthyneura. Mol. Phylogenet. Evol., 38: 459-469. https://doi.org/10.1016/j.ympev.2005.08.017

Kochzius, M., C. Seidel, A. Antoniou, S.K. Botla, D. Campo, A. Cariani, E. García-Vazquez, J. Hauschild, C. Hervet, S. Hjörleifsdottir, G. Hreggvidsson, K. Kappel, M. Landi, A. Magoulas, V. Marteinsson, M. Nölte, S. Planes, F. Tinti, C. Turan, M.N. Venugopal, H. Weber & D. Blohm. 2010. Identifying fishes through DNA barcodes and microarrays. PLoS ONE, 5(9): e12620. https://doi.org/10.1371/journal.pone.0012620

Kurabayashi, A. & R. Ueshima. 2000. Complete sequence of the mitochondrial DNA of the primitiveop isthobranch gastropod Pupa strigosa: systematic implication of the genome organization. Mol. Biol. Evol., 17: 266-277. https://doi.org/10.1093/oxfordjournals.molbev.a026306

Lewontin, R.C. & J.L. Hubby. 1966. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics, 54:595-609. https://doi.org/10.1093/genetics/54.2.595

Liu, Y. & Z. Cui. 2010a. The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda. Comp. Biochem. Phys. D, 5: 190-198. https://doi.org/10.1016/j.cbd.2010.04.001

Liu Y. & Z. Cui. 2010b. Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods. Mol. Biol. Rep., 37: 2559-2569. https://doi.org/10.1007/s11033-009-9773-2

Lowenstein, J.H., G. Amato & S.-O. Kolokotronis. 2009. The real maccoyii: Identifying tuna sushi with DNA barcodes - Contrasting characteristic attributes and genetic distances. PLoS ONE, 4(11): e7866. https://doi.org/10.1371/journal.pone.0007866

Lowenstein, J.H., J. Burger, C.W. Jeitner, G. Amato, S-O. Kolokotronis & M. Gochfeld. 2010. DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers. Biol. Lett., 6: 692-695. https://doi.org/10.1098/rsbl.2010.0156

Marine Barcode of Life (MarBOL). 2015. http:// www.marinebarcoding.org/.

Márquez, C., M. Elías-Gutiérrez & F. Vergara-Silva. 2010. Base de datos de los códigos de barra de la vida. 167-169, en: Memorias del Congreso Nacional de Genética 2010. Sociedad Mexicana de Genética y FES-Iztacala, UNAM.

Márquez, C. 2011. Códigos de barras de DNA y marcadores moleculares. 142-148, en: Memorias del Congreso Nacional de Genética 2011. Sociedad Mexicana de Genética y Universidad de las Américas (ISBN 978-607-02-3097-4).

Miller, A.D. & C.M. Austin. 2006. The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic in vestigation of the Decapod using mitochondrial sequences. Mol. Phylogenet. Evol., 38 (3): 565- 574. https://doi.org/10.1016/j.ympev.2005.10.001

Mora, C., D.P. Tittensor, S. Adl, A.G.B. Simpson & B. Worm. 2011. How many species are there on earth and in the ocean? Plos Biol. 9(8): e1001127. https://doi.org/10.1371/journal.pbio.1001127

National Center for Biotechnology Information (GenBank, NCBI). 2015. http://www.ncbi.nlm. nih.gov/.

Pett, W., J.F. Ryan, K. Pang, J.C. Mullikin, M.Q. Martindale, A.D. Baxevanis & D.V. Lavrov. 2011. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insights from mtDNA and the nuclear genome. Mitochondr. DNA, 22:130-142. https://doi.org/10.3109/19401736.2011.624611

Polar Barcode of Life (PolarBOL). 2015. http:// www.polarbarcoding.org/.

Prosser S., A. Martínez-Arce & M. Elías-Gutiérrez. 2013. A new set of primer for COI amplification from freshwater microcrustaceans. Mol. Ecol. Resour. 13: 1151-1155. https://doi.org/10.1111/1755-0998.12132

Radulovici, A.E., P. Archambault & F. Dufresne. 2010. DNA Barcodes for Marine Biodiversity: Moving Fast Forward?. Diversity 2: 450-472. https://doi.org/10.3390/d2040450

Reaka-Kudla, M.L. 1997. The global biodiversity of coral reefs: A comparison with rain forests. 83-108, en: Reaka-Kudla, M.L., D.E. Wilson, & E.O.Wilson. (Eds.) Biodiversity II. Understanding and Protecting Our Biological Resources. Joseph Henry Press, Washington, D.C.

Richards, V.P., M.J. Stanhope & M.S. Shivji. 2012. Island endemism, morphological stasis, and possible cryptic speciation in two coral reef, commensal Leucothoid amphipod species throughout Florida and the Caribbean. Biodivers. Conserv., 21:343-361. https://doi.org/10.1007/s10531-011-0186-x

Saitoh K., K. Hayashizaki, Y. Yokoyama, T. Asahida, H. Toyohara & Y. Yamashita. 2000. Complete nucleotide sequence of itochon flounder (Paralichthys olivaceus) mitochondrial genome: Structural properties and cue for resolving teleostean relationships. J. Hered., 91: 271- 278. https://doi.org/10.1093/jhered/91.4.271

Scouras, A. & M.J. Smith. 2006. The complete mitochondrial genomes of the sea lily Gymnocrinus richeri and the feather star Phanogenia gracilis: signature nucleotide bias and unique nad4L gene rearrangement within crinoids. Mol. Phylogenet. Evol. 39: 323-334. https://doi.org/10.1016/j.ympev.2005.11.004

Shen, X., J. Ren, Z. Cui, Z. Sha, B. Wang, J. Xiang & B. Liu. 2007. The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene, 403: 98-109. https://doi.org/10.1016/j.gene.2007.06.021

Shen, X., M. Sun, Z. Wu, M. Tian, H. Cheng, F. Zhao & X. Meng. 2009a. The complete mitochondrial genome of the ridge tail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes. Gene, 437 (1-2): 1-8. https://doi.org/10.1016/j.gene.2009.02.014

Shen, X., M. Tian, Z. Liu, H. Cheng, J. Tan, X. Meng & J. Ren. 2009b. Complete mitochondrial genome of the sea cucumber Apostichopus japonicas (Echinodermata: Holothuroidea): The first representative from the subclass Aspidochirotacea with the echinoderm ground pattern. Gene, 439: 79-86. https://doi.org/10.1016/j.gene.2009.03.008

Shen, X., H. Wang, J. Ren, M. Tian & M. Wang. 2010. The mitochondrial genome of Euphausia superba (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers. Mol. Biol. Rep., 37: 771-784. https://doi.org/10.1007/s11033-009-9602-7

Smith, PJ., D. Steinke, A. Dettai, P. McMillan, D. Welsford, A. Stewart & R. D. Ward. 2012. DNA barcodes and species identifications in Ross Sea and Southern Ocean Fishes. Polar. Biol., 35:1297-1310. https://doi.org/10.1007/s00300-012-1173-8

Sponge Barcoding Project (spongebarcoding.org). 2015. http://www.palaeontologie.geo.unimuenchen.de/SBP/.

Swinstrom K., R. Caldwell, M.H. Fourcade & J.L. Boore. 2005. The first complete mitochondrial genome sequences for stomatopod crustaceans: implications for phylogeny. Secuencias enviadas directamente a NCBI. Manuscrito No publicado. University of California, Berkley. https://doi.org/10.2172/960399

Teletchea, F. 2010. After 7 years and 1000 citations: Comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists. Mitochondr. DNA, 21: 206-226. https://doi.org/10.3109/19401736.2010.532212

The Canadian Centre for DNA Barcoding (CCDB). 2015. http://www.ccdb.ca/.

Uthicke, S., M. Byrne & C. Conand. 2010. Genetic barcoding of commercial Beˆche-de-mer species (Echinodermata:Holothuroidea). Mol. Ecol. 10: 634-646. https://doi.org/10.1111/j.1755-0998.2009.02826.x

Valdez-Moreno, M., L.Vásquez-Yeomans, M. ElíasGutiérrez, N.V. Ivanova & P.D. N. Hebert. 2010. Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatán Peninsula, México: potential in fisheries management. Mar. Freshwater Res., 61(6): 655-671. https://doi.org/10.1071/MF09222

Valdez-Moreno, M., C. Quintal-Lizama, R. GómezLozano & M.C., García-Rivas. 2012. Monitoring an alien invasion: DNA barcoding and the identification of lionfish and their prey on coral reefs of the Mexican Caribbean. PLoS ONE 7(6): e36636. https://doi.org/10.1371/journal.pone.0036636

Vargas, S., A. Schuster, K. Sacher, G. Büttner, S. Schätzle, B. Läuchli. K. Hall, J.N.A. Hooper, D. Erpenbeck & G. Wörheide. 2012. Barcoding sponges: An overview based on comprehensive sampling. PLoS ONE, 7(7):e39345. https://doi.org/10.1371/journal.pone.0039345

Williams, S.T., P.G. Foster & D.T.J. Littlewood. 2014. The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene, 533: 38-47. https://doi.org/10.1016/j.gene.2013.10.005

Wilson, E.O. 1992. The Diversity of Life. W.W. Norton, N.Y., 424 p.

Wilson, K., V. Cahill, E. Ballment & J. Benzie. 2000. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Mol. Biol. Evol., 17 (6): 863-874. https://doi.org/10.1093/oxfordjournals.molbev.a026366

Descargas

Publicado

2015-12-31

Cómo citar

Márquez, C. (2015). Aplicación de los códigos de barras de DNA en el descubrimiento de la diversidad animal marina. CICIMAR Oceánides, 30(2), 35–52. https://doi.org/10.37543/oceanides.v30i2.150

Número

Sección

Artículos