Abstract
The wedge clam Donax trunculus is an Atlantic-Mediterranean warm-temperate species found from Senegal to the northern coast of France, including the Mediterranean and Black Sea. It is commercially exploited in several European countries and constitutes an important fishing resource due to its high economical value. To contribute to its conservation and management, nineteen microsatellite markers were isolated from two enriched genomic libraries. These loci were characterized in 30 clams from a single population from northwest Spain. The number of alleles per locus ranged from 2 to 17 and observed and expected heterozygosity varied from zero to 0.714 and from 0.078 to 0.950, respectively. Linkage disequilibrium was not detected and nine loci were in agreement with Hardy–Weinberg equilibrium. Fifteen polymorphic markers were arranged into three multiplex PCR sets to reduce both time and cost of microsatellite genotyping. This is the first time that polymorphic microsatellite markers have been reported for D. trunculus. These new markers provide a valuable resource for future population genetics studies and management and culture of this species.
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Tebble N (1966) British bivalve seashells. A handbook for identification. Trustees of the British Museum (Natural History), Edinburgh
Bayed A, Guillou J (1985) Contribution to the study of populations of the Donax genus: the population of Donax trunculus L. (Mollusca, Bivalvia). Ann Inst Oceanogr 61(2):139–147
Gaspar MB, Ferreira R, Monteiro CC (1999) Growth and reproductive cycle of Donax trunculus L., (Mollusca : Bivalvia) off Faro, southern Portugal. Fish Res 41(3):309–316
Chícharo L, Chícharo A, Gaspar M, Alves F, Regala J (2002) Ecological characterization of dredged and non-dredged bivalve fishing areas off south Portugal. J Mar Biol Assoc UK 82(1):41–50
Vale P, Sampayo MAD (2002) Evaluation of marine biotoxin’s accumulation by Acanthocardia tuberculatum from Algarve, Portugal. Toxicon 40(5):511–517
Zeichen MM, Agnesi S, Mariani A, Maccaroni A, Ardizzone GD (2002) Biology and population dynamics of Donax trunculus L. (Bivalvia: Donacidae) in the South Adriatic Coast (Italy). Est Coast Shelf Sci 54(6):971–982
Thébaud O, Véron G, Fifas S (2005) Incidences des épisodes d’efflorescences de micro algues toxiques sur les écosystèmes et sur les pêcheries de coquillages en baie de Douarnenez. In: Rapport Ifremer R.INT.DCB/DEM – DCB/STH/UDPP 05-010. Brest, France, pp 88
Ramón M, Cano J, Peña JB, Campos MJ (2005) Current status and perspectives of mollusc (bivalves and gastropods) culture in the Spanish Mediterranean. Bol Inst Esp Oceanogr 21:361–373
Molares J, Parada JM, Navarro-Pérez E, Fernández A (2008) Variabilidad interanual de las ventas de los principales recursos marisqueros de Galicia y su relación con las condiciones ambientales. Rev Gal Rec Mar (Art Inf Tecn) 2(1):1–42
Martínez-Patiño D, Nóvoa S, Ojea J, Rodríguez E (2003) Determinación de la talla de primera maduración sexual de la coquina, Donax trunculus (Linné, 1758) (Mollusca:Bivalvia), en un banco natural de la Ría del Barquero (NO Galicia). In: Libro de Actas IX Congreso Nacional de Acuicultura. Consejería de Agricultura y Pesca. Junta de Andalucía, pp 215–217
Bert TM, Crawford CR, Tringali MD, Seyoum S, Galvin JL, Higham M, Lund C (2007) Genetic management of hatchery-based stock enhancement. In: Bert TM (ed) Ecological and genetic implications of aquaculture activities. Springe, Dordrecht, pp 123–174
Holsinger KE, Gottlieb LD (1991) Conservation of rare and endangered plants—principles and prospects. In: Falk DA, Holsinger KE (eds) Genetics and conservation of rare plants. Oxford University Press, New York, pp 195–208
Martínez L, Arias A, Méndez J, Insua A, Freire R (2009) Development of twelve polymorphic microsatellite markers in the edible cockle Cerastoderma edule (Bivalvia: Cardiidae). Conserv Genet Resour 1(1):107–109
Pereira SM, Arias A, Méndez J, Insua A, Freire R (2010) Isolation of twelve microsatellite markers in the pullet carpet shell Venerupis pullastra (Bivalvia: Veneridae). Conserv Genet Resour 2:201–203
Arias-Pérez A, Fernández-Tajes J, Gaspar MB, Méndez J (2012) Isolation of microsatellite markers and analysis of genetic diversity among east atlantic populations of the sword razor shell Ensis siliqua: a tool for population management. Biochem Genet 50(5–6):397–415
Porta J, Porta JM, Martínez-Rodríguez G, Álvarez MD (2006) Development of a microsatellite multiplex PCR for Senegalese sole (Solea senegalensis) and its application to broodstock management. Aquaculture 256(1–4):159–166
Fernández-Tajes J, Méndez J (2007) Identification of the razor clam species Ensis arcuatus, E. siliqua, E. directus, E. macha, and Solen marginatus using PCR-RFLP analysis of the 5S rDNA region. J Agric Food Chem 55(18):7278–7282
Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10(4):506–513
Billote N, Lagoda PJL, Risterucci AM, Baurens FC (1999) Microsatellite-enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–288
Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20(5):758–760
Meglécz E (2007) MICROFAMILY (version 1): a computer program for detecting flanking-region similarities among different microsatellite loci. Mol Ecol Notes 7(1):18–20
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573–580
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89(3):583–590
Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier
Raymond M, Rousset F (1995) Genepop (version-1.2)—population-genetics software for exact tests and ecumenicism. J Hered 86(3):248–249
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43(1):223–225
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4(3):535–538
Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5(3):453–455
Holleley CE, Geerts PG (2009) Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46(7):511–517
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11(1):1–16
Reece KS, Ribeiro WL, Gaffney PM, Carnegie RB, Allen SK (2004) Microsatellite marker development and analysis in the eastern oyster (Crassostrea virginica): confirmation of null alleles and non-Mendelian segregation ratios. J Hered 95(4):346–352
Evans BS, Knauer J, Taylor JJU, Jerry DR (2006) Development and characterization of six new microsatellite markers for the silver- or gold-lipped pearl oyster, Pinctada maxima (Pteriidae). Mol Ecol Notes 6(3):835–837
Arias A, Freire R, Méndez J, Insua A (2010) Isolation and characterization of microsatellite markers in the queen scallop Aequipecten opercularis and their application to a population genetic study. Aquat Living Resour 23(2):199–207
Néve G, Meglécz E (2000) Microsatellite frequencies in different taxa. Trends Ecol Evol 15(9):376–377
Meglécz E, Petenian F, Danchin E, Coeur d’Acier A, Rasplus JY, Faure E (2004) High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera: Parnassius apollo and Euphydryas aurinia. Mol Ecol 13(6):1693–1700
Cruz F, Pérez M, Presa P (2005) Distribution and abundance of microsatellites in the genome of bivalves. Gene 346:241–247
Meglécz E, Anderson SJ, Bourguet D, Butcher R, Caldas A, Cassel-Lundhagen A, Coeur d’Acier A, Dawson DA, Faure N, Fauvelot C, Franck P, Harper G, Keyghobadi N, Kluetsch C, Muthulakshmi M, Nagaraju J, Patt A, Petenian F, Silvain JF, Wilcock HR (2007) Microsatellite flanking region similarities among different loci within insect species. Insect Mol Biol 16(2):175–185
McInerney CE, Allcock AL, Johnson MP, Bailie DA, Prodoehl PA (2011) Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs. Heredity 106(1):78–87
Jia M, Li J, Wang S (2010) Isolation and characterization of 18 polymorphic microsatellite loci from freshwater pearl mussel (Cristaria plicata). Conserv Genet 11(3):1131–1133
Arias A, Freire R, Pablo De La Roche J, Román G, Méndez J, Insua A (2011) Identification, inheritance, and variation of microsatellite markers in the black scallop Mimachlamys varia. Biochem Genet 49(3–4):139–152
Xiao J, Cordes JF, Jones KC, Reece KS (2008) Eleven novel microsatellite markers for the Asian oyster Crassostrea ariakensis. Mol Ecol Resour 8(4):843–845
Launey S, Ledu C, Boudry P, Bonhomme F, Naciri-Graven Y (2002) Geographic structure in the European flat oyster (Ostrea edulis L.) as revealed by microsatellite polymorphism. J Hered 93(5):331–338
Zouros E, Foltz DW (1984) Possible Explanations of heterozygote deficiency in bivalve mollusks. Malacologia 25(2):583–591
Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24(3):621–631
Vadopalas B, Leclair LL, Bentzen P (2004) Microsatellite and allozyme analyses reveal few genetic differences among spatially distinct aggregations of geoduck clams (Panopea abrupta, Conrad 1849). J Shellfish Res 23(3):693–706
Munguia-Vega A, Soria G, Pfister T, Cudney-Bueno R (2010) Isolation and characterization of microsatellite loci in the rock scallop (Spondylus calcifer) (Bivalvia: Spondylidae) from the Northern Gulf California, Mexico. Conserv Genet Resour 2(1):51–54
Sell J, Mioduchowska M, Kaczmarczyk A, Szymanczak R (2013) Identification and characterization of the first microsatellite loci for the thick-shelled river mussel Unio crassus (Bivalvia: Unionidae). J Exp Zool A 319(2):113–116
Acknowledgments
We thank Dra. Dorotea Martínez and Susana Nóvoa from Centro de Cultivos Marinos de Ribadeo—CIMA (Xunta de Galicia) for supplying the wedge clam samples, Jose García Gil for his technical assistance and Luisa Martínez for helpful comments on earlier versions of this manuscript. We would also like to thank Dr. James D. Austin for their revision of English grammar and style. This work was supported by the Consellería de Economía e Industria (Xunta de Galicia) through project 10MMA103013 and by Ministerio de Educación through a predoctoral FPU fellowship awarded to Ana Nantón.
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Nantón, A., Arias-Pérez, A., Méndez, J. et al. Characterization of nineteen microsatellite markers and development of multiplex PCRs for the wedge clam Donax trunculus (Mollusca: Bivalvia). Mol Biol Rep 41, 5351–5357 (2014). https://doi.org/10.1007/s11033-014-3406-0
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DOI: https://doi.org/10.1007/s11033-014-3406-0