Molecular identification of native oysters on the coast of Maranhão, Brazil
DOI:
https://doi.org/10.20950/1678-2305.2018.44.4.377Keywords:
mitochondrial DNA, COI, species identificationAbstract
Oysters are found along the whole coast of Brazil. The phenotypes of the species vary considerably according to the characteristics of the habitat. The present study investigated the existence of different oyster species of the genus Crassostrea on the coast of Maranhão, using the Multiplex PCR technique and DNA Barcoding. The results of the Multiplex PCR revealed two distinct bands characteristic of the species C. gasar and C. rhizophorae in a total of 135 samples analyzed. The sequencing of the COI gene of 98 samples produced a 695 bp fragment and 15 haplotypes for C. gasar and 640 bp and eight haplotypes for C. rhizophorae. The haplotype tree divided the two species clearly into different clades with 100% bootstrap support. Intraspecific genetic divergence was 0.2% in both species, while interspecific divergence was 23.6%. The similarity between the sequences generated and those available in BoldSystems ranged from 97.01% to 98.37% for C. rhizophorae and from 97.55% to 99.84% for both C. gasar and C. brasiliana, reinforcing the taxonomic problems in this group, which supports the synonymization of these species. The DNA barcoding permitted the reliable identification of the samples and confirmed the existence of two species of oyster in the study area.References
BONDIOLI, A.C.V.; MARQUES, R.C.; TOLEDO, L.F.A.; BARBIERI, E. 2017 PCR-RFLP for identification of the pearl oyster Pinctada imbricate from Brazil and Venezuela. Boletim do Instituto de Pesca, 43(3): 459-463.
CARVALHO, D. D.; SEERIG, A.; MELO, D. D.; SOUSA, A. B.; PIMENTA, D.; OLIVEIRA, D. A. A. 2008 Identificação molecular de peixes: o caso do Surubim (Pseudoplatystoma spp.). Revista Brasileira de Reprodução Animal, 32(4): 215í 219.
CAVALEIRO, N. P.; SOLÉ-CAVA, A. M.; LAZOSKI, C.; CUNHA, H. A. 2013 Polymorphic microsatellite loci for two Atlantic oyster species: Crassostrea rhizophorae and C. gasar. Molecular biology reports 40(12): 7039-7043.
CAVALLI, R. O.; FERREIRA, J. F. 2010 O futuro da pesca da aquicultura marinha no Brasil: a maricultura. Ciência e Cultura, 629(3): 38-39.
CHRISTO, S. W.; ABSHER, T. M. 2006 Reproductive period of Crassostrea rhizophorae (Guilding, 1828) and Crassostrea brasiliana (Lamark, 1819) (Bivalvia:Ostreidae) in Guaratuba bay, Paraná, Brazil. Journal of Coastal Research, 2(39): 1215-1218.
CYWINSKA, A.; HUNTER, F. F.; HEBERT, P. D. 2006 Identifying Canadian mosquito species through DNA barcodes. Medical and veterinary entomology, 20(4): 413-424.
FELSENSTEIN, J. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4): 783-791.
FOLMER, O.; BLACK, M.; HOEH, W.; LUTZ, R. VRIJENHOEK, R. 1994 DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3(5): 294í 299.
GALVÃO, M.S.; PEREIRA, O.M.; HILSDORF, A.W. 2013 Molecular identification and distribution of mangrove oysters (Crassostrea) in an estuarine ecosystem in Southeast Brazil: implications for aquaculture and fisheries management. Aquaculture Research, 44(10): 1589-1601.
GALVÃO, M.S.N.; ALVES, P.M.F.; HILSDORF, A.W.S. 2017 First record of the Saccostrea oyster in Bertioga, São Paulo, Brazil. Boletim do Instituto de Pesca, 43(4): 638-645.
GARDUNHO, D.C.L.; GOMES, C.P.; TAGLIARO, C.H.; BEASLEY, C.R. 2012 Settlement of an unidentified oyster (Crassostrea) and other epibenthos on plastic substrates at a northern Brazilian mangrove island. Brazilian Journal of Aquatic Science and Technology, 16(1): 41-51.
HALL, T.A. 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95 âÂ"ž 98 âÂ"ž NT. Nucleic Acids Symposium Series, 41(41): 95í 98.
HEBERT, P. D.; RATNASINGHAM, S.; DE WAARD, J. R. 2003 Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sciences, 270 (Suppl 1): S96-S99.
IGNACIO, B.L.; ABSHER, T.M.; LAZOSKI, C.; SOLE´-CAVA, A.M. 2000 Genetic evidence of the presence of two species of Crassostrea (Bivalvia: Ostreidae) on the coast of Brazil. Marine Biology, 136(6): 987í 991.
LAPEGUE, S.; BOUTET, I.; LEITÃO, A.; HEURTEBISI, S.; GARCIA, P.; THIRIOTUIE-VREUX, C.; BOUDRY, P. 2002 Trans-Atlantic distribution of a mangrove oyster species revealed by 16S mtDNA and karyological analyses. Biology Bull, 202(3): 232-242.
LAZOSKI, C.; GUSMÃO, J.; BOUDRY, P.; SOLE´-CAVA, A.M. 2011 Phylogeny and phylogeography of Atlantic oyster species: evolutionary history, limited genetic connectivity and isolation by distance. Marine Ecology Progress Series, 426: 197í 212.
LIBRADO, P.; ROZAS, J. 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11): 1451-1452.
LUDWIG, S.; PATELLA, R.; STOIEV, S.; CASTILHO-WESTPHAL, G.; GIROTTO, M. V.; OSTRENSKY, A. 2011 A molecular method to detect and identify the native species of southwestern Atlantic Crassostrea (Mollusca: Ostreidae). Zoologia (Curitiba), 28(4): 420-426.
MEDRANO, J. F.; AASEN, E.; SHARROW, L. 1990 DNA extraction from nucleated red blood cells. Biotechniques, 8(1): 43.
MELO, A. G. C. D.; VARELA, E. S.; BEASLEY, C. R.; SCHNEIDER, H.; SAMPAIO, I.; GAFFNEY, P. M.; TAGLIARO, C. H. 2010 Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea). Genetics and Molecular Biology, 33(3): 564-572.
MELO, M.A.D.; SILVA, A.R.B.; BEASLEY, C.R.; TAGLIARO, C.H. 2013 Multiplex species-specific PCR identification of native and non-native oysters (Crassostrea) in Brazil: a useful tool for application in oyster culture and stock management. Aquaculture International, 21(06): 1325í 1332.
PIE, M. R.; RIBEIRO, R. O.; BOEGER, W. A.; OSTRENSKY, A.; FALLEIROS, R. M.; ANGELO, L. 2006 A simple PCRâ€ÂRFLP method for the discrimination of native and introduced oyster species (Crassostrea brasiliana, C. rhizophorae and C. gigas; Bivalvia: Ostreidae) cultured in Southern Brazil. Aquaculture Research, 37(15): 1598-1600.
REECE, K. S.; CORDES, J. F.; STUBBS, J. B.; HUDSON, K. L.; FRANCIS, E. A. 2008 Molecular phylogenies help resolve taxonomic confusion with Asian Crassostrea oyster species. Marine Biology, 153(4): 709í 721.
RIOS, E. C. 1994 Sea shells of Brazil. 2ª ed. Rio Grande: Fundação Universidade do Rio Grande. 492p.
SAITOU, N.; NEI, M. 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4): 406í 425.
SANGER, F.; NICKLEN, S.; COULSON, A. R. 1977 DNA sequencing with chain-terminating inhibitors. Proceedings of the national academy of sciences, 74(12): 5463-5467.
SIMONE, L. R. L.; DO AMARAL, V. S. 2014 Revision of genus Crassostrea (Bivalvia: Ostreidae) of Brazil. Journal of the Marine Biological Association of the United Kingdom, 94(4): 811-836.
SOLÉ-CAVA, A. M. 2008 Códigos de barra de DNA: o rabo que abana o cachorro. Ciência Hoje, 41(245): 65-67.
SOLÉ-CAVA, A. M.; Wí–RHEIDE, G. 2007 The perils and merits (or the Good, the Bad and the Ugly) of DNA barcoding of sponges í a controversial discussion. In: CUSTÓDIO, M.R.; LÔBO-HAJDU G.; HAJDU, E.; MURICY G. (ed.) Porifera research: biodiversity, innovation and sustainability. Série Livros (28). Rio de Janeiro: Museu Nacional. p. 603í 612.
TAMURA, K.; STECHER, G.; PETERSON, D.; FILIPSKI, A.; KUMAR, S. 2013 MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution, 30(12): 2725-2729.
THOMPSON, J. D.; HIGGINS, D. G.; GIBSON, T. J. 1994 Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 22(22): 4673-4680.
VARELA, E.S; BEASLEY, C.R.; SCHNEIDER, H.; SAMPAIO, I.; MARQUES-SILVA, N.S.; TAGLIARO, C.H. 2007 Molecular phylogeny of mangrove oysters (Crassostrea) from Brazil. Journal of molluscan studies, 73(3): 229-234.
WAKAMATSU, T. 1973 A ostra de Cananéia e o seu cultivo. São Paulo: Instituto Oceanográfico, Universidade de São Paulo. 141 p.
CARVALHO, D. D.; SEERIG, A.; MELO, D. D.; SOUSA, A. B.; PIMENTA, D.; OLIVEIRA, D. A. A. 2008 Identificação molecular de peixes: o caso do Surubim (Pseudoplatystoma spp.). Revista Brasileira de Reprodução Animal, 32(4): 215í 219.
CAVALEIRO, N. P.; SOLÉ-CAVA, A. M.; LAZOSKI, C.; CUNHA, H. A. 2013 Polymorphic microsatellite loci for two Atlantic oyster species: Crassostrea rhizophorae and C. gasar. Molecular biology reports 40(12): 7039-7043.
CAVALLI, R. O.; FERREIRA, J. F. 2010 O futuro da pesca da aquicultura marinha no Brasil: a maricultura. Ciência e Cultura, 629(3): 38-39.
CHRISTO, S. W.; ABSHER, T. M. 2006 Reproductive period of Crassostrea rhizophorae (Guilding, 1828) and Crassostrea brasiliana (Lamark, 1819) (Bivalvia:Ostreidae) in Guaratuba bay, Paraná, Brazil. Journal of Coastal Research, 2(39): 1215-1218.
CYWINSKA, A.; HUNTER, F. F.; HEBERT, P. D. 2006 Identifying Canadian mosquito species through DNA barcodes. Medical and veterinary entomology, 20(4): 413-424.
FELSENSTEIN, J. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4): 783-791.
FOLMER, O.; BLACK, M.; HOEH, W.; LUTZ, R. VRIJENHOEK, R. 1994 DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3(5): 294í 299.
GALVÃO, M.S.; PEREIRA, O.M.; HILSDORF, A.W. 2013 Molecular identification and distribution of mangrove oysters (Crassostrea) in an estuarine ecosystem in Southeast Brazil: implications for aquaculture and fisheries management. Aquaculture Research, 44(10): 1589-1601.
GALVÃO, M.S.N.; ALVES, P.M.F.; HILSDORF, A.W.S. 2017 First record of the Saccostrea oyster in Bertioga, São Paulo, Brazil. Boletim do Instituto de Pesca, 43(4): 638-645.
GARDUNHO, D.C.L.; GOMES, C.P.; TAGLIARO, C.H.; BEASLEY, C.R. 2012 Settlement of an unidentified oyster (Crassostrea) and other epibenthos on plastic substrates at a northern Brazilian mangrove island. Brazilian Journal of Aquatic Science and Technology, 16(1): 41-51.
HALL, T.A. 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95 âÂ"ž 98 âÂ"ž NT. Nucleic Acids Symposium Series, 41(41): 95í 98.
HEBERT, P. D.; RATNASINGHAM, S.; DE WAARD, J. R. 2003 Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sciences, 270 (Suppl 1): S96-S99.
IGNACIO, B.L.; ABSHER, T.M.; LAZOSKI, C.; SOLE´-CAVA, A.M. 2000 Genetic evidence of the presence of two species of Crassostrea (Bivalvia: Ostreidae) on the coast of Brazil. Marine Biology, 136(6): 987í 991.
LAPEGUE, S.; BOUTET, I.; LEITÃO, A.; HEURTEBISI, S.; GARCIA, P.; THIRIOTUIE-VREUX, C.; BOUDRY, P. 2002 Trans-Atlantic distribution of a mangrove oyster species revealed by 16S mtDNA and karyological analyses. Biology Bull, 202(3): 232-242.
LAZOSKI, C.; GUSMÃO, J.; BOUDRY, P.; SOLE´-CAVA, A.M. 2011 Phylogeny and phylogeography of Atlantic oyster species: evolutionary history, limited genetic connectivity and isolation by distance. Marine Ecology Progress Series, 426: 197í 212.
LIBRADO, P.; ROZAS, J. 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11): 1451-1452.
LUDWIG, S.; PATELLA, R.; STOIEV, S.; CASTILHO-WESTPHAL, G.; GIROTTO, M. V.; OSTRENSKY, A. 2011 A molecular method to detect and identify the native species of southwestern Atlantic Crassostrea (Mollusca: Ostreidae). Zoologia (Curitiba), 28(4): 420-426.
MEDRANO, J. F.; AASEN, E.; SHARROW, L. 1990 DNA extraction from nucleated red blood cells. Biotechniques, 8(1): 43.
MELO, A. G. C. D.; VARELA, E. S.; BEASLEY, C. R.; SCHNEIDER, H.; SAMPAIO, I.; GAFFNEY, P. M.; TAGLIARO, C. H. 2010 Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea). Genetics and Molecular Biology, 33(3): 564-572.
MELO, M.A.D.; SILVA, A.R.B.; BEASLEY, C.R.; TAGLIARO, C.H. 2013 Multiplex species-specific PCR identification of native and non-native oysters (Crassostrea) in Brazil: a useful tool for application in oyster culture and stock management. Aquaculture International, 21(06): 1325í 1332.
PIE, M. R.; RIBEIRO, R. O.; BOEGER, W. A.; OSTRENSKY, A.; FALLEIROS, R. M.; ANGELO, L. 2006 A simple PCRâ€ÂRFLP method for the discrimination of native and introduced oyster species (Crassostrea brasiliana, C. rhizophorae and C. gigas; Bivalvia: Ostreidae) cultured in Southern Brazil. Aquaculture Research, 37(15): 1598-1600.
REECE, K. S.; CORDES, J. F.; STUBBS, J. B.; HUDSON, K. L.; FRANCIS, E. A. 2008 Molecular phylogenies help resolve taxonomic confusion with Asian Crassostrea oyster species. Marine Biology, 153(4): 709í 721.
RIOS, E. C. 1994 Sea shells of Brazil. 2ª ed. Rio Grande: Fundação Universidade do Rio Grande. 492p.
SAITOU, N.; NEI, M. 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4): 406í 425.
SANGER, F.; NICKLEN, S.; COULSON, A. R. 1977 DNA sequencing with chain-terminating inhibitors. Proceedings of the national academy of sciences, 74(12): 5463-5467.
SIMONE, L. R. L.; DO AMARAL, V. S. 2014 Revision of genus Crassostrea (Bivalvia: Ostreidae) of Brazil. Journal of the Marine Biological Association of the United Kingdom, 94(4): 811-836.
SOLÉ-CAVA, A. M. 2008 Códigos de barra de DNA: o rabo que abana o cachorro. Ciência Hoje, 41(245): 65-67.
SOLÉ-CAVA, A. M.; Wí–RHEIDE, G. 2007 The perils and merits (or the Good, the Bad and the Ugly) of DNA barcoding of sponges í a controversial discussion. In: CUSTÓDIO, M.R.; LÔBO-HAJDU G.; HAJDU, E.; MURICY G. (ed.) Porifera research: biodiversity, innovation and sustainability. Série Livros (28). Rio de Janeiro: Museu Nacional. p. 603í 612.
TAMURA, K.; STECHER, G.; PETERSON, D.; FILIPSKI, A.; KUMAR, S. 2013 MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution, 30(12): 2725-2729.
THOMPSON, J. D.; HIGGINS, D. G.; GIBSON, T. J. 1994 Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 22(22): 4673-4680.
VARELA, E.S; BEASLEY, C.R.; SCHNEIDER, H.; SAMPAIO, I.; MARQUES-SILVA, N.S.; TAGLIARO, C.H. 2007 Molecular phylogeny of mangrove oysters (Crassostrea) from Brazil. Journal of molluscan studies, 73(3): 229-234.
WAKAMATSU, T. 1973 A ostra de Cananéia e o seu cultivo. São Paulo: Instituto Oceanográfico, Universidade de São Paulo. 141 p.
Downloads
Published
2018-12-26
Issue
Section
Scientific Article
