Abstract
Scallops (Bivalvia, Pectinidae) are among the most valuable source of marine food. With about 350 extant species distributed worldwide and a total global production comprising 18 species, the development of proper species-level identification assays is imperative. DNA barcoding has proven to be a useful tool in species identification. A partial region at the 5′ end of the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as the “Folmer region,” was proposed as the most suitable DNA barcoding marker. However, Folmer primers have failed to amplify polymerase chain reaction (PCR) products in different organisms, including scallops. Searching for an alternative barcoding gene region, we analyzed the complete mitochondrial 16S rRNA gene in 15 scallop species. We found that the interspecific variation at the 5′ end is twice as high as that at the 3′ end. Based on that evidence, we designed a novel Pectinidae family-specific primer set, aiming to amplify a partial region at the 5′ end of the 16S rRNA gene, and tested its suitability as a barcoding tool. A neighbor-joining analysis identified correctly 100 % of the scallop specimens analyzed, with high bootstrap support. Our new primers are well suited for DNA barcoding analysis and may contribute to scallop food industry surveys, as well as routine taxonomic surveys.
Similar content being viewed by others
References
FAO (2014) FishStatJ: software for fishery statistical time series. FAO Fisheries and Aquaculture Department, Statistics and Information Service
FAO (2014). Fishery and aquaculture statistics yearbook 2012. FAO, Rome. http://www.fao.org/3/a-i3740t.pdf. Last accessed 2 Sept 2014
The Ministry of Agriculture, Forestry and Fisheries of Japan (MAFF) (2014) The 88th statistical yearbook of Ministry of Agriculture. Forestry and Fisheries, MAFF
Marín A, Fujimoto T, Arai K (2013) Rapid species identification of fresh and processed scallops by multiplex PCR. Food Control 32:472–476
Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc B 270:313–321
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. Mol Mar Biol Biotechnol 3:294–299
Blankenship LE, Yayanos AA (2005) Universal primers and PCR of gut contents to study marine invertebrate diets. Mol Ecol 14:891–899
Kim SJ, Lee KY, Ju SJ (2013) Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding. Mol Ecol Resour 13:781–787
Pochon X, Smith KF, Bott NJ et al (2013) Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS One 8:e73935
Lobo J, Costa P, Teixeira M, Ferreira M, Costa M, Costa F (2013) Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans. BMC Ecol 13:34
Schubart CD (2009) Mitochondrial DNA and decapod phylogenies: the importance of pseudogenes and primer optimization. In: Martin JW et al (eds) Decapod crustacean phylogenetics. CRC Press Taylor & Francis group, Boca Raton, pp 47–65
Chen J, Li Q, Kong L, Yu H (2011) How DNA barcodes complement taxonomy and explore species diversity: the case study of a poorly understood marine fauna. PLoS One 6:e21326
Feng Y, Li Q, Zheng X (2011) DNA barcoding and phylogenetic analysis of Pectinidae (Mollusca: bivalvia) based on mitochondrial COI and 16S rRNA genes. Mol Biol Rep 38:291–299
Will KW, Mishler BD, Wheeler QD (2005) The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol 54:844–851
Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites D (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool 2:5
Palumbi SR, Martin AP, Romano S, McMillan WO, Stice L, Grabowski G (1991) The simple fool’s guide to PCR. Department of Zoology-University of Hawaii, Special Publication, Honolulu
Barucca M, Olmo E, Schiaparelli S, Canapa A (2004) Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA. Mol Phylogenet Evol 31:89–95
Canapa A, Barucca M, Marinelli A, Olmo E (2000) Molecular data from the 16S rRNA gene for the phylogeny of Pectinidae. (Mollusca: Bivalvia). J Mol Evol 50:93–97
Malkowsky Y, Klussmann-Kolb A (2012) Phylogeny and spatio-temporal distribution of European Pectinidae (Mollusca: Bivalvia). Syst Biodivers 10:233–242
Plazzi F, Passamonti M (2010) Towards a molecular phylogeny of Mollusks: Bivalves’ early evolution as revealed by mitochondrial genes. Mol Phylogenet Evol 57:641–657
Puslednik L, Serb JM (2008) Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology. Mol Phylogenet Evol 48:1178–1188
Saavedra C, Peña JB (2006) Phylogenetics of American scallops (Bivalvia: Pectinidae) based on partial 16S and 12S ribosomal RNA gene sequences. Mar Biol 150:111–119
Kong XY, Yu ZN, Liu YJ, Chen LL (2003) Intraspecific genetic variation in mitochondrial 16S ribosomal gene of Zhikong scallop Chlamys farreri. J Shellfish Res 22:655–660
Mahidol C, Na-Nakorn U, Sukmanomon S, Yoosuk W, Taniguchi N, Nguyen TTT (2007) Phylogenetic relationships among nine scallop species (Bivalvia: Pectinidae) inferred from nucleotide sequences of one mitochondrial and three nuclear gene regions. J Shellfish Res 26:25–32
Yuan T, He M, Huang L (2009) Intraspecific genetic variation in mitochondrial 16S rRNA and COI genes in domestic and wild populations of Huaguizhikong scallop Chlamys nobilis Reeve. Aquaculture 289:19–25
Marín A, Fujimoto T, Arai K (2013) Genetic structure of the Peruvian scallop Argopecten purpuratus inferred from mitochondrial and nuclear DNA variation. Mar Genomics 9:1–8
Sokolov EP (2000) An improved method for DNA isolation from mucopolysaccharide-rich molluscan tissues. J Mollusc Stud 66:573–575
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Stothard P (2000) The Sequence Manipulation Suite: javascript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102–1104
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Geller J, Meyer C, Parker M, Hawk H (2013) Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Mol Ecol Resour 13:851–861
Meyer CP (2003) Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biol J Linn Soc 79:401–459
Matsumoto M, Hayami I (2000) Phylogenetic analysis of the family Pectinidae (Bivalvia). J Mollusc Stu 66:477–488
Iserte JA, Stephan BI, Goñi SE, Borio CS, Ghiringhelli PD, Lozano ME (2013) Family-specific degenerate primer design: A tool to design consensus degenerated oligonucleotides. Biotechnol Res Int Article ID 383646. doi:10.1155/2013/383646
Bower SM, Carnegie RB, Goh B, Jones SRM, Lowe GJ, Mak MWS (2004) Preferential PCR ampification of protistan small subunit rDNA from metazoan tissues. J Euk Microbiol 51:325–332
Sonnenberg R, Nolte AW, Tautz D (2007) An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Front Zool 4:6
Zarowiecki MZ, Huyse T, Littlewood DTJ (2007) Making the most of mitochondrial genomes–Markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes: Digenea). Int J Parasitol 37:1401–1418
Song H, Buhay JE, Whiting MF, Crandall KA (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci USA 105:13486–13491
Kim M, Morrison M, Yu Z (2010) Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J Microbiol Methods 84:81–87
Yang L, Tan Z, Wang D, Xue L, Guan M, Huang T, Li R (2014) Species identification through mitochondrial rRNA genetic analysis. Sci Rep 4:4089. doi:10.1038/srep04089
Terranova MS, Brutto SL, Arculeo M, Mitton JB (2007) A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic species. J Zool Syst Evol Res 45:289–298
Saavedra C, Peña JB (2004) Phylogenetic relationships of commercial European and Australasian king scallops (Pecten spp.) based on partial 16S ribosomal RNA gene sequences. Aquaculture 235:153–166
Jozefowicz CJ, O´Foighil D (1998) Phylogenetic analysis of southern hemisphere flat oysters based on partial mitochondrial 16S rDNA gene sequences. Mol Phylogenet Evol 10:426–435
Wu X, Li X, Yu Z (2013) The mitochondrial genome of the scallop Mimachlamys senatoria (Bivalvia. Mitochondrial DNA, Pectinidae). doi:10.3109/19401736.2013.823181
Wu X, Xu X, Yu Z, Kong X (2009) Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets. BMC Res Notes 2:69
Ren JF, Shen X, Jiang F, Liu B (2010) The mitochondrial genomes of two scallops, Argopecten irradians and Chlamys farreri (Mollusca: Bivalvia): the most highly rearranged gene order in the family Pectinidae. J Mol Evol 70:57–68
Smith DR, Snyder M (2007) Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome. J Mol Evol 65:380–391
Acknowledgments
We wish to thank Ms. Shelah Buen-Ursua (SEAFDEC/AQD, the Philippines), Prof. Kazuo Inaba (University of Tsukuba, Japan), Dr. Kenta Suda (Okabe Co. Ltd., Japan) and Dr. Suzu Fujimoto (Hakodate College of Technology, Japan) for providing scallop and mussel samples; and Dr. Noriko Azuma (Hokkaido University, Japan) for her support during sequence analyses.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is a link to electronic supplementary material.
Supporting information
Table S1 List of primers used in the amplification of the complete 16S rRNA mitochondrial gene in seven scallop species.
Rights and permissions
About this article
Cite this article
Marín, A., Fujimoto, T. & Arai, K. The variable 5′ end of the 16S rRNA gene as a novel barcoding tool for scallops (Bivalvia, Pectinidae). Fish Sci 81, 73–81 (2015). https://doi.org/10.1007/s12562-014-0819-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12562-014-0819-6