Abstract
Nineteen polymorphic microsatellite loci were developed for the collector sea urchin, Tripneustes gratilla. Microsatellite enriched genomic libraries were constructed and subsequently sequenced using Roche 454 technology. The 19 loci were characterized in 24 individuals from the Indonesian archipelago. Observed levels of heterozygosity ranged from 0.21–0.92 with a mean of 12.2 alleles per locus. No pairs of loci showed evidence of significant linkage disequilibrium and 5 loci significantly deviated from Hardy–Weinberg expectations.
References
Boutin-Ganache I, Raposo M, Raymond M, Deschepper CF (2001) M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques 31:24–28
Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2010) Geneious v5.5, Available from http://www.geneious.com. Accessed 3 April 2012
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10:564–567
Glenn TC, Schable NA (2005) Isolating microsatellite DNA Loci. Meth Enzy 395:202–222
Meglecz E, Costedoat C, Dubut V et al (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26:403–404
Mous PJ, Pet JS, Arifin Z, Djohani R, Erdmann MV, Halim A, Knight M, Pet-Soede L, Wiadnya G (2005) Policy needs to improve marine capture fisheries management and to define a role for marine protected areas in Indonesia. Fish Manag and Ecol 12:259–268
Palumbi SR (2003) Population genetics, demographic connectivity, and the design of marine reserves. Ecol Appl 13:S146–S158
Planes S, Jones GP, Thorrold SR (2009) Larval dispersal connects fish populations in a network of marine protected areas. Proc Natl Acad Sci 106:5693–5697
Rozen S, Skaletsky H (1999) Primer3 on the WWW for general users and for biologist programmers. Meth Mol Biol 132:365–386
Sala E, Aburto-Oropeza O, Paredes G, Parra I, Barrera JC, Dayton PK (2002) A general model for designing networks of marine reserves. Science 298:1991–1993
Toonen RJ (1997) Microsatellites for ecologists: non-radioactive isolation and amplification protocols for microsatellite markers.http://www2.hawaii.edu/~toonen/files/Msats-for-Ecologists-V1.pdf Accessed 3 April 2012
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 10:506–513
Acknowledgments
We thank the Indonesian government, the Indonesian Institute of Sciences (LIPI) and RISTEK for collection permits, 0085/SIP/FRP/SM/V/2010 and 0133/SIP/FRP/SM/V/2010 under which all collections were made in full accordance with Indonesian laws and regulations. A special thank you is reserved for Mr Onny Nurrahman Marwayana and Ms Hagi Yulia Sugeha. Funding for this work was provided in part by the TOTAL Foundation, University of Hawai‘i Graduate Student Organization, University of Hawai‘i Arts and Sciences Student Research Award, University of Hawai‘i Edmondson Grant, Sigma XI Grants In Aid of Research, The Explorers Club, The Rufford Small Grants Foundation and the University of Hawai‘i NSF-EPSCoRprogram (Investing in Multidisciplinary University Activities, EPS-0903833, J. Gaines, PI) in support of the core functional genomics facility at the Hawai‘i Institute of Marine Biology. This is HIMB contribution # 1500 and The School for Ocean and Earth Science and Technology contribution # 8684.
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Wainwright, B.J., Arlyza, I.S. & Karl, S.A. Isolation and characterization of nineteen microsatellite loci for the collector sea urchin, Tripneustes gratilla . Conservation Genet Resour 4, 963–965 (2012). https://doi.org/10.1007/s12686-012-9683-9
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DOI: https://doi.org/10.1007/s12686-012-9683-9