Abstract
DNA barcoding is a versatile approach that has revolutionized taxonomy and other akin topics in biology and ecology, due to its simplicity and relatively costless procedures. The method consists in the production of one or a few amplicons from informative genetic regions via Sanger sequencing. These markers are selected because they tend to evolve at a similar pace as speciation, allowing to discriminate organismal species. The applicability of this technique is here portrayed for the taxonomical identification of marine sponges (phylum: Porifera) as an exemplification.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Huxley J (1940) The new systematics. Oxford University Press, London
Schuh RT (2000) Biological systematics: principles and applications. Cornell University Press, New York
Simpson GG (1961) Principles of animal taxonomy. Columbia University Press, New York
Folmer O, Black M, Hoeh W et al (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3(5):294–299
Hebert PDN, Cywinska A, Ball SL et al (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270(1512):313–321
Paulay G, Meyer Christopher P (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3(12):e422
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains archaea, bacteria, and Eucarya. Proc Natl Acad Sci U S A 87(12):4576–4579
Savolainen V, Cowan RS, Vogler AP et al (2005) Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philos Trans R Soc Lond Ser B Biol Sci 360(1462):1805–1811
Schoch CL, Seifert KA, Huhndorf SRV et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci U S A 109(16):6241–6246
Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765–4774
Creer S, Fonseca VG, Porazinska DL et al (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol Ecol 19(SUPPL. 1):4–20
Creer S, Deiner K, Frey S et al (2016) The ecologist’s field guide to sequence-based identification of biodiversity. Methods Ecol Evol 7(9):1008–1018
Xavier JR, Rachello-Dolmen PG, Parra-Velandia F et al (2010) Molecular evidence of cryptic speciation in the “cosmopolitan” excavating sponge Cliona celata (Porifera, Clionaidae). Mol Phylogenet Evol 56:13–20
Erpenbeck D, Hooper JNA, Wörheide G (2006) CO1 phylogenies in diploblasts and the “barcoding of life” - are we sequencing a suboptimal partition? Mol Ecol Notes 6:550–553
Wörheide G, Nichols S, Goldberg J (2004) Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): Implications for phylogenetic studies. Mol Phylogenet Evol 33(3):816–830
Chombard C, Boury-Esnault N, Tillier S (1998) Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data. Syst Biol 47:351–366
Boury-Esnault N, Rützler K (1997) Thesaurus of sponge morphology. In: Smithsonian contributions to zoology. Smithsonian Institution Press, Washington, DC, pp 1–55
Hooper JNA (2003) Sponguide. Guide to sponge collection and identification. http://www.qmuseum.qld.gov.au/organisation/sections/SessileMarineInvertebrates/index.asp
Hooper JNA, Van Soest RWM (eds) (2002) Systema Porifera. A guide to the classification of sponges, vol 1&2. Kluwer Academic/Plenum Publishers, New York, p 1708
de Voogd NJ, Alvarez B, Boury-Esnault N, Carballo JL, Cárdenas P, Díaz MC, Dohrmann M, Downey R, Hajdu E, Hooper JNA, Kelly M, Klautau M, Manconi R, Morrow CC, Pisera AB, RÚos P, Rützler K, Schönberg C, Vacelet J, van Soest RWM (2022). World Porifera Database. https://www.marinespecies.org/porifera on 2022-03-03. https://doi.org/10.14284/359. Accessed May 2021
Towbin H, Staehelin T, Gordon J (1979) Electrophoretic transfer of proteins from polyacrylamide gels to NC sheets: procedure and applications. Proc Natl Acad Sci U S A 76:4350–4354
Acknowledgments
Thanks are due to R. Pannone, E. d’Aniello, C. La Vecchia, E. Mauriello, and M. L. Palomba for laboratory advice and support.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Núñez-Pons, L., Mazzella, V., Rispo, F., Efremova, J., Calcinai, B. (2022). DNA Barcoding Procedures for Taxonomical and Phylogenetic Studies in Marine Animals: Porifera as a Case Study. In: Verde, C., Giordano, D. (eds) Marine Genomics. Methods in Molecular Biology, vol 2498. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2313-8_10
Download citation
DOI: https://doi.org/10.1007/978-1-0716-2313-8_10
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2312-1
Online ISBN: 978-1-0716-2313-8
eBook Packages: Springer Protocols