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Aplysina (Porifera: Demospongiae) species identification through SSCP-ITS patterns

Published online by Cambridge University Press:  24 November 2009

Flávia Rachel M. Lamarão ,
Estéfane C. Reis ,
Tatiana A. Simão ,
Rodolpho M. Albano  and
Gisele Lôbo-Hajdu
Flávia Rachel M. Lamarão
Affiliation:
Departamento de Genética, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier, 524—PHLC—Sala 205, 20550-013, Rio de Janeiro, RJ, Brazil Departamento de Hanseníase, IOC, Fiocruz, Avenida Brasil, 4365—Manguinhos, 21040-360, Rio de Janeiro, RJ, Brazil Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Avenida 28 de Setembro, 87 (fundos, 4° andar), 20551-013, Rio de Janeiro, RJ, Brazil
Estéfane C. Reis
Affiliation:
Departamento de Genética, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier, 524—PHLC—Sala 205, 20550-013, Rio de Janeiro, RJ, Brazil
Tatiana A. Simão
Affiliation:
Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Avenida 28 de Setembro, 87 (fundos, 4° andar), 20551-013, Rio de Janeiro, RJ, Brazil
Rodolpho M. Albano
Affiliation:
Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Avenida 28 de Setembro, 87 (fundos, 4° andar), 20551-013, Rio de Janeiro, RJ, Brazil
Gisele Lôbo-Hajdu*
Affiliation:
Departamento de Genética, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier, 524—PHLC—Sala 205, 20550-013, Rio de Janeiro, RJ, Brazil
*
Correspondence should be addressed to: G. Lôbo-Hajdu, Departamento de Genética, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier, 524—PHLC—Sala 205, 20550-013, Rio de Janeiro, RJ, Brazil email: glhajdu@uerj.br
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Abstract

Keratose sponges have no spicules and limited robust morphological characters, causing severe problems for taxonomic classification. Single-strand conformational polymorphism (SSCP) analysis of PCR amplified internal transcribed spacers (ITS) of nuclear ribosomal RNA (rRNA) genes was used to elucidate speciation patterns in marine sponges of the genus Aplysina. In this study, Aplysina species with non-ambiguous traditional morphological alpha taxonomy were used to generate standard SSCP-ITS patterns, which were compared with patterns from alleged new species. Our results show that ITS-SSCP patterns allowed the differentiation of Aplysina sponges, demonstrating the advantage of a method that explores the secondary structure compared to direct sequencing.

Keywords

marine spongesinternal transcribed spacersPCR-SSCPcryptic species
Type
Research Article
Information
Journal of the Marine Biological Association of the United Kingdom , Volume 90 , Issue 4 , June 2010 , pp. 845 - 850
Copyright
Copyright © Marine Biological Association of the United Kingdom 2009

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References

REFERENCES

Alvarez, B., Krishnan, M. and Gibb, K. (2007) Analysis of intragenomic variation of the rDNA internal transcribed spacers (ITS) in Halichondrida (Porifera: Demospongiae). Journal of the Marine Biological Association of the United Kingdom 87, 1599–1605.CrossRefGoogle Scholar
Arnheim, N. (1983) Concerted evolution of multi-gene families. In Nei, M. and Koehn, R.K. (eds) Evolution of genes and proteins. Sunderland, MA: Sinauer Associates, pp. 38–61.Google Scholar
Bassam, B.J., Caetano-Anolles, G. and Gresshoff, P.M. (1991) Fast and sensitive silver staining of DNA in polyacrilamide gels. Analytical Biochemistry 196, 80–83.CrossRefGoogle Scholar
Bergquist, P.R. and Cook, S.C. (2002a) Order Verongida Bergquist, 1978. In Hooper, J.N.A. and van Soest, R.W.M. (eds) Systema Porifera: a guide to the classification of sponges. New York: Kluwer Academic/Plenum Publishers, pp. 1081–1096.CrossRefGoogle Scholar
Bergquist, P.R. and Cook, S.C. (2002b) Family Aplysinidae Carter, 1875. In Hooper, J.N.A. and van Soest, R.W.M. (eds) Systema Porifera: a guide to the classification of sponges. New York: Kluwer Academic/Plenum Publishers, pp. 1082–1085.CrossRefGoogle Scholar
Colombo, F., Mangiagalli, G. and Renon, P. (2005) Identification of tuna species by computer-assisted and cluster analysis of PCR-SSCP electrophoretic patterns. Food Control 16, 51–53.CrossRefGoogle Scholar
Deprés, L., Kruger, F.J., Imbert, E.B. and Adamson, M.L. (1995) ITS-2 ribosomal RNA indicates Schistossoma hippopotami is a distinct species. International Journal for Parasitology 25, 1509–1514.Google Scholar
Duran, S., Giribet, G. and Turon, X. (2004) Phylogeographical history of the sponge Crambe crambe (Porifera, Poecilosclerida): range expansion and recent invasion of the Macaronesian Islands from the Mediterranean Sea. Molecular Ecology 13, 109–122.CrossRefGoogle ScholarPubMed
Giribet, G. and Wheeler, W.C. (2002) On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data. Invertebrate Biology 121, 271–324.CrossRefGoogle Scholar
Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41, 95–98.Google Scholar
Heim, I., Nickel, M. and Brümmer, F. (2007) Molecular markers for species discrimination in poriferans: a case study on species of the genus Aplysina. In Custódio, M.R., Lôbo-Hajdu, G., Hajdu, E. and Muricy, G. (eds) Porifera research: biodiversity, innovation and sustainability. Rio de Janeiro: Série Livros 28, Museu Nacional, pp. 361–371.Google Scholar
Hillis, D.M. (1987) Molecular versus morphological approaches to systematics. Annual Review of Ecology and Systematics 18, 23–42.Google Scholar
Hoshino, S., Saito, D.S. and Fujita, T. (2008) Contrasting genetic structure of two Pacific Hymeniacidon species. Hydrobiologia 603, 313–326.Google Scholar
Lôbo-Hajdu, G., Lamarão, F.R.M., Guimarães, A.C.R., Salgado, A., Vieiralves, T., Mansure, J.J. and Albano, R.M. (2002) A low-cost and quick method to distinguish Porifera species on the basis of ITS sequence variation revealed by PCR-single-strand conformation polymorphism (SSCP). Bolletino dei Musei e degli Istituti Biologici dell Università di Genova 117, 66–67.Google Scholar
Lôbo-Hajdu, G., Guimarães, A.C.R., Salgado, A., Lamarão, F.R.M., Vieiralves, T., Mansure, J.J. and Albano, R.M. (2004) ITS sequence variation in Porifera revealed by PCR-Single-Strand Conformation Polymorphism (PCR-SSCP). Bolletino dei Musei e degli Istituti Biologici dell Università di Genova 68, 413–423.Google Scholar
Lopez, J.V., Peterson, C.L., Willoughby, R., Wright, A.E., Enright, E., Zoladz, S., Reed, J.K. and Pomponi, S.A. (2002) Characterization of genetic markers for in vitro cell line identification of the marine sponge Axinella corrugata. Journal of Heredity 93, 27–36.CrossRefGoogle ScholarPubMed
Malhotra, A. and Thorpe, R.S. (2004) Maximizing information in systematic revisions: a combined molecular and morphological analysis of a cryptic green pitviper complex (Trimeresurus stejnegeri). Biological Journal of the Linnean Society of London 82, 219–235.Google Scholar
Moritz, C. and Hillis, D.M. (1996) Molecular Systematics: context and controversies. In Hillis, D.M., Moritz, C. and Mable, B.K. (eds) Molecular systematics. Sunderland, MA: Sinauer Associates, pp. 1–13.Google Scholar
Nichols, S.A. and Barnes, P.A.G. (2005) A molecular phylogeny and historical biogeography of the marine sponge genus Placospongia (Phylum Porifera) indicate low dispersal capabilities and widespread crypsis. Journal of Experimental Marine Biology and Ecology 323, 81–96.CrossRefGoogle Scholar
Orita, M., Suzuki, Y., Sekiya, T. and Hayashi, K. (1989) Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5, 874–879.CrossRefGoogle ScholarPubMed
Patterson, C., Williams, D.M. and Humphries, C.J. (1993) Congruence between molecular and morphological phylogenies. Annual Review of Ecology and Systematics 24, 153–188.CrossRefGoogle Scholar
Pinheiro, U.S. and Hajdu, E. (2001) Shallow-water Aplysina Nardo (Aplysinidae, Verongida, Demospongiae) from the São Sebastião Channel and its environs (Tropical southwestern Atlantic), with the description of a new species and a literature review of other Brazilian records of the genus. Revista Brasileira de Zoologia 18, 143–160.CrossRefGoogle Scholar
Pinheiro, U.S., Hajdu, E. and Custódio, M.R. (2007) Aplysina Nardo (Porifera, Verongida, Aplysinidae) from the Brazilian coast with description of eight new species. Zootaxa 1609, 1–51.CrossRefGoogle Scholar
Schmitt, S., Hentschel, U., Zea, S., Dandekar, T. and Wolf, M. (2005) ITS2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). Journal of Molecular Evolution 60, 327–336.CrossRefGoogle ScholarPubMed
Soto, D. and Sukumar, S. (1992) Improved detection of mutations in the p53 gene in human tumors as single-stranded conformation polymorphs and double-stranded heteroduplex DNA. Genome Research 2, 96–98.CrossRefGoogle ScholarPubMed
Sunnucks, P., Wilson, A.C.C., Beheregaray, L.B., Zenger, K., French, J. and Taylor, A.C. (2000) SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Molecular Ecology 9, 1699–1710.CrossRefGoogle Scholar
van Soest, R.M.W. (1994) Demosponge distribution patterns. In van Soest, R.W.M., van Kempen, T.M.G. and Braekman, J.C. (eds) Sponges in time and space. Proceedings of the 4th International Porifera Congress. Rotterdam: Balkema Publishers, pp. 213–223.Google Scholar
Vidigal, T.H.D.A., Caldeira, R.L., Simpson, A.J.G. and Carvalho, O.S. (2000) Further studies on the molecular systematics of Biomphalaria snails from Brazil. Memórias do Instituto Oswaldo Cruz 95, 57–66.CrossRefGoogle ScholarPubMed
Vidigal, T.H.D.A., Magalhães, K.G., Caldeira, R.L., Simpson, A.J.G. and Carvalho, O.S. (2002) A multiplex-PCR approach to identification of the Brazilian intermediate host of Schistossoma mansoni. Memórias do Instituto Oswaldo Cruz 97, 95–97.CrossRefGoogle Scholar
Vink, C.J. and Paterson, A.M. (2003) Combined molecular and morphological phylogenetic analyses of the New Zealand wolf spider genus Anoteropsis (Araneae: Lycosidae). Molecular Phylogenetics and Evolution 28, 576–587.CrossRefGoogle ScholarPubMed
Wörheide, G., Nichols, S.A. and Goldberg, J. (2004) Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies. Molecular Phylogenetics and Evolution 33, 816–830.CrossRefGoogle ScholarPubMed
Zhu, X., D'Amelio, S., Paggi, L. and Gasser, R.B. (2000) Assessing sequence variation in the internal transcribed spacers of ribossomal DNA whitin and among members of the Contracaecum osculatum complex (Nematoda: Ascaridoidea: Anisakidae). Parasitology Research 86, 677–683.CrossRefGoogle Scholar