Asolation and characterization of new microsatellite markers for the cortés geoduck (Panopea globosa)
DOI:
https://doi.org/10.37543/oceanides.v31i1.162Keywords:
Microsatellites, Next Generation Sequencing, Panopea globosa, Cortés GeoduckAbstract
The geoduck Panopea globosa is a long-lived and large endemic infaunal clam sustaining a growing fishery in the Northwest coast of México that, in spite of its increasing demand in Asian markets very little is known about its biology. In order to provide genetic markers to support genetic research of wild populations, nine novel microsatellite loci (di-, tri-, and tetranucleotide repeats) were developed using shotgun sequencing
with next generation technology (Illumina). The number of alleles per locus ranged from 3 to 16 and the observed and expected heterozygosity ranged from 0.286 to 0.650 and 0.504 to 0.906, respectively. Five loci were found to be significantly deviated from the Hardy-Weinberg equilibrium and three pairs showed evidence of linkage disequilibrium. Most loci are highly informative for population genetics and linkage analyses according to their
polymorphism information content (> 0.5) and will be useful for increasing our understanding of the wild population structure and developing a sustainable fishery management..
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Abdelkrim, J., B. Robertson, J. A. Stanton & N. Gemmell. 2009. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques, 46 (3): 185-192. https://doi.org/10.2144/000113084
Amos, W., J. I. Hoffman, A. Frodsham, L. Zhang, S. Best & A. V. S. Hill. 2007. Automated binning of microsatellite alleles: problems and solutions. Mol. Ecol. Notes, 7 (1): 10-14. https://doi.org/10.1111/j.1471-8286.2006.01560.x
Bahassi, E. & P. J. Stambrook. 2014. Next-generation sequencing technologies: breaking the sound barrier of human genetics. Mutagenesis, 29 (5): 303-310. https://doi.org/10.1093/mutage/geu031
Becquet, V., I. Lanneluc, B. Simon-Bouhet & P. Garcia. 2009. Microsatellite markers for the Baltic clam, Macoma balthica (Linne, 1758), a key species concerned by changing southern limit, in exploited littoral ecosystems. Conserv. Genet. Resour., 1 (1): 265-267. https://doi.org/10.1007/s12686-009-9065-0
Chakraborty, R., M. Kimmel, D. N. Stivers, L. J. Davison & R. Deka. 1997. Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. P. Natl. Acad. Sci. USA, 94 (3): 1041-1046. https://doi.org/10.1073/pnas.94.3.1041
Cruz-Hernández, P., A. Munguía-Vega, I. Leyva-Valencia, F. Lucero-Burquez & D. B. Lluch-Cota. 2014. Development of 24 tetra-nucleotide microsatellite markers in Cortes Geoduck Panopea globosa by next-generation sequencing. Conserv. Genet. Resour., 6 (3): 531-533. https://doi.org/10.1007/s12686-014-0172-1
de Arruda, M. P., E. C. Gonçalves, M. P. C. Schneider, A. L. D. C. da Silva & E. Morielle-Versute. 2010. An alternative genotyping method using dye-labeled universal primer to reduce unspecific amplifications. Mol. Biol. Rep., 37 (4): 2031-2036. https://doi.org/10.1007/s11033-009-9655-7
Estoup, A. & J. M. Cornuet. 1999. Microsatellite evolution: inferences from population data. 49- 65, In: Goldstein, D. B. , Schlötterer, C. (eds.). Microsatellites: Evolution and Applications. Oxford University Press, Oxford. Excoffier, L., G. Laval & S. Schneider. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolut. Bioinform. Online, 1: 47-50. https://doi.org/10.1177/117693430500100003
Faircloth, B. C. 2008. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol. Ecol. Resour., 8 (1): 92-94. https://doi.org/10.1111/j.1471-8286.2007.01884.x
Guichoux, E., L. Lagache, S. Wagner, P. Chaumeil, P. Leger, O. Lepais, C. Lepoittevin, T. Malausa, E. Revardel, F. Salin & R. J. Petit. 2011. Current trends in microsatellite genotyping. Mol. Ecol. Resour., 11 (4): 591-611. https://doi.org/10.1111/j.1755-0998.2011.03014.x
Hedgecock, D., G. Li, S. Hubert, K. Bucklin & V. Ribes. 2004. Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster, Crassostrea gigas. J. Shellfish Res., 23 (2): 379-385.
Lance, S. L., C. N. Love, S. O. Nunziata, J. R. O'Bryhim, D. E. Scott, R. W. Flynn & K. L. Jones. 2013. 32 species validation of a new Illumina paired-end approach for the development of microsatellites. PLoS One, 8 (11): e81853. https://doi.org/10.1371/journal.pone.0081853
McInerney, C. E., A. L. Allcock, M. P. Johnson, D. A. Bailie & P. A. Prodohl. 2011. Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs. Heredity, 106 (1): 78-87. https://doi.org/10.1038/hdy.2010.36
Munguia-Vega, A., I. Leyva-Valencia, D. B. Lluch-Cota & P. Cruz-Hernández. 2015. Genetic structure of the Cortes Geoduck Panopea globosa Dall, 1898, from the Mexican Northwest. J. Shellfish Res., 34 (1): 153-161. https://doi.org/10.2983/035.034.0119
Nunziata, S. O., J. D. Karron, R. J. Mitchell, S. L. Lance, K. L. Jones & D. W. Trapnell. 2012. Characterization of 42 polymorphic microsatellite loci in Mimulus ringens (Phrymaceae) using Illumina sequencing. Am. J. Bot., 99 (12): E477-E480. https://doi.org/10.3732/ajb.1200180
O'Bryhim, J., J. P. Chong, S. L. Lance, K. L. Jones & K. J. Roe. 2012. Development and characterization of sixteen microsatellite markers for the federally endangered species: Leptodea leptodon (Bivalvia: Unionidae) using paired-end Illumina shotgun sequencing. Conserv. Genet. Resour., 4 (3): 787-789. https://doi.org/10.1007/s12686-012-9644-3
Park, S. 2001. MStools v 3 (Excel spreadsheet toolkit for data conversion). Smurfit Institute of Genetics. Trinity College, Dublin.
Schlotterer, C. 2004. The evolution of molecular markers - just a matter of fashion? Nat. Rev. Genet., 5 (1): 63-69. https://doi.org/10.1038/nrg1249
Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol., 18 (2): 233-234. https://doi.org/10.1038/72708
Selkoe, K. A. & R. J. Toonen. 2006. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett., 9 (5): 615-629. https://doi.org/10.1111/j.1461-0248.2006.00889.x
Šidák, Z. K. 1967. Rectangular confidence regions for the means of multivariate normal distributions. J. Am. Stat. Assoc., 62 (318): 626-633. https://doi.org/10.1080/01621459.1967.10482935
Suárez-Moo, P. J., L. E. Calderon-Aguilera, H. Reyes Bonilla, G. Díaz-Erales, V. Castañeda-Fernandez-de-Lara, E. A. Aragón-Noriega & A. Rocha-Olivares. 2013. Integrating genetic, phenotypic and ecological analyses to assess the variation and clarify the distribution of the Cortes Geoduck (Panopea globosa). J. Mar. Biol. Assoc. U. K., 93 (3): 809-816. https://doi.org/10.1017/S0025315412001464
Van Oosterhout, C., W. F. Hutchinson, D. P. M. Wills & P. Shipley. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes, 4 (3): 535-538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
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Copyright (c) 2016 Celia Isabel Bisbal -Pardo, Miguel íngel Del Río -Portilla, Ana Yonori Castillo -Paéz, Axayácatl Rocha-Olivares
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