Isolation and characterisation of eighteen microsatellite markers from the sea cucumber Holothuria scabra (Echinodermata : Holothuriidae)
Alison J. Fitch A , Grant Leeworthy B , Xiaoxu Li C , Will Bowman D , Luke Turner D and Michael G. Gardner A E F
+ Author Affiliations
- Author Affiliations
A School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
B Tasmanian Seafoods Pty Ltd, 13–17 Redgum Drive, Dandenong South, Vic. 3175, Australia.
C SARDI Aquatic Sciences, PO Box 120, Henley Beach, SA 5022, Australia.
D Tasmanian Seafood Pty Ltd, PO Box 38795, Winnellie, NT 0821, Australia.
E Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5001, Australia.
F Corresponding author. Email: michael.gardner@flinders.edu.au
Australian Journal of Zoology 60(6) 368-371 https://doi.org/10.1071/ZO12114
Submitted: 8 November 2012 Accepted: 9 March 2013 Published: 3 April 2013
Abstract
We isolated 18 new, polymorphic, microsatellite markers from Holothuria scabra, a commercially important species of sea cucumber found throughout the Asia-Pacific region. Next-generation sequencing was used to identify 206 unique loci for which primers were designed. Of these unique loci, we trialled 65 primer pairs in the target species, and 48 (74%) amplified a product of the expected size. Eighteen loci were found to be polymorphic and reliable, and were screened for variation in 50 individuals, from a single population from Croker Island, Northern Territory, Australia. Observed heterozygosity ranged from 0.00 to 0.96 (mean = 0.46) and the number of alleles per locus from 2 to 28 (mean = 9.61). These loci will be useful for the investigation of population structure and mating systems in H. scabra and may also be of use in other holothurian species.
Additional keywords: GS-FLX, next-generation sequencing.
References
Addison, J. A., and Hart, M. W. (2005). Spawning, copulation and inbreeding coefficients in marine invertebrates. Biology Letters 1, 450–453.| Spawning, copulation and inbreeding coefficients in marine invertebrates.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD28jhtVKqsg%3D%3D&md5=67cf0d77548ac231a1ecd226860d5d0aCAS |
Battaglene, S. C., and Bell, J. D. (2004). The restocking of sea cucumbers in the Pacific Islands. Marine Ranching. FAO Fishery Technical Paper No. 429.
Chang, Y., Feng, Z., Yu, J., and Ding, J. (2009). Genetic variability analysis in five populations of the sea cucumber Stichopus (Apostichopus) japonicus from China, Russia, South Korea and Japan as revealed by microsatellite markers. Marine Ecology (Berlin) 30, 455–461.
| Genetic variability analysis in five populations of the sea cucumber Stichopus (Apostichopus) japonicus from China, Russia, South Korea and Japan as revealed by microsatellite markers.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXkt1OjtA%3D%3D&md5=3faf23d827d1dfe53b3ed7a41408acb5CAS |
Chen, J. (2004). Present status and prospects of sea cucumber industry in China. Advances in sea cucumber aquaculture and management. In ‘Advances in Sea Cucumber Aquaculture and Management’. (Eds A. Lovatelli, C. Conand, S. Purcell, S. Uthicke, J.-F. Hamel and A. Mercier.) pp. 269–272. FAO Fisheries Technical Paper No. 463 (FAO: Rome.)
D’Silva, D. (2001). The Torres Strait bêche de mer (sea cucumber) fishery. Secretariat of the Pacific Community Bêche de Mer Information Bulletin No. 31.
Dailianis, T., Tsigenopoulos, C. S., Dounas, C., and Voultsiadou, E. (2011). Genetic diversity of the imperilled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation. Molecular Ecology 20, 3757–3772.
| Genetic diversity of the imperilled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC3Mfit1emtg%3D%3D&md5=d22704f4359204606cf1a1035817b302CAS |
Doyle, J. J., and Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19, 11–15.
Faircloth, B. C. (2008). MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8, 92–94.
| MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXivVSitL8%3D&md5=cbe40398bb3af83ba9b0b0362378bfc7CAS |
Friedman, K., Eriksson, H., Tardy, E., and Pakoa, K. (2011). Management of sea cucumber stocks: patterns of vulnerability and recovery of sea cucumber stocks impacted by fishing. Fish and Fisheries 12, 75–93.
| Management of sea cucumber stocks: patterns of vulnerability and recovery of sea cucumber stocks impacted by fishing.Crossref | GoogleScholarGoogle Scholar |
Gamboa, R., Gomez, A. L., and Nieveales, M. F. (2004). The status of sea cucumber fishery and mariculture in the Philippines. Advances in sea cucumber aquaculture and management. In ‘Advances in Sea Cucumber Aquaculture and Management’. (Eds A. Lovatelli, C. Conand, S. Purcell, S. Uthicke, J.-F. Hamel and A. Mercier.) pp. 269–272. FAO Fisheries Technical Paper No. 463. (FAO: Rome.)
Gardner, M. G., Fitch, A. J., Bertozzi, T., and Lowe, A. J. (2011). Rise of the machines – recommendations for ecologists when using second generation sequencing for microsatellite development. Molecular Ecology Resources 11, 1093–1101.
| Rise of the machines – recommendations for ecologists when using second generation sequencing for microsatellite development.Crossref | GoogleScholarGoogle Scholar |
Hamilton, R., and Lokani, P. (2011). Severely overfished sea cucumbers in the autonomous region of Bougainville. Secretariat of the Pacific Community Bêche de mer Information Bulletin No. 31.
Hayden, M. J., Nguyen, T. M., Waterman, A., McMichael, G. L., and Chalmers, K. J. (2008). Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat. Molecular Breeding 21, 271–281.
| Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXitlyrs74%3D&md5=a10aa6007350cbfb58e60176e708d493CAS |
Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6, 65–70.
Kalinowski, S., Taper, M., and Marshall, T. (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16, 1099–1106.
| Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.Crossref | GoogleScholarGoogle Scholar |
Kang, J.-H., Kim, Y.-K., Kim, M.-J., Park, J.-Y., An, C.-M., Kim, B.-S., Jun, J.-C., and Kim, S.-K. (2011). Genetic differentiation among populations and colour variants of sea cucumbers (Stichopus japonicus) from Korea and China. International Journal of Biological Sciences 7, 323–332.
| Genetic differentiation among populations and colour variants of sea cucumbers (Stichopus japonicus) from Korea and China.Crossref | GoogleScholarGoogle Scholar |
Meglécz, E. (2007). MICROFAMILY (version 1): a computer program for detecting flanking-region similarities among different microsatellite loci. Molecular Ecology Notes 7, 18–20.
| MICROFAMILY (version 1): a computer program for detecting flanking-region similarities among different microsatellite loci.Crossref | GoogleScholarGoogle Scholar |
Plutchak, L. L., Simmons, R. E., and Woodruff, D. S. (2006). Multilocus allozyme heterozygote deficiencies in Crepidula onyx: geographic and temporal patterns among adult snails in Mission Bay, California. The Journal of Molluscan Studies 72, 337–348.
| Multilocus allozyme heterozygote deficiencies in Crepidula onyx: geographic and temporal patterns among adult snails in Mission Bay, California.Crossref | GoogleScholarGoogle Scholar |
Raymond, M., and Rousset, F. (1995). GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. The Journal of Heredity 86, 248–249.
Rozen, S., and Skaletsky, H. J. (2000). PRIMER3 on the WWW for general users and for biologist programmers. In ‘Bioinformatics Methods and Protocols: Methods in Molecular Biology’. (Eds S. Krawetz and S. Misener.) pp. 365–386. (Humana Press: New Jersey.)
Uthicke, S., Welch, D., and Benzie, J. A. H. (2004). Slow growth and lack of recovery in overfished holothurians on the Great Barrier Reef: evidence from DNA fingerprints and repeated large-scale surveys. Conservation Biology 18, 1395–1404.
| Slow growth and lack of recovery in overfished holothurians on the Great Barrier Reef: evidence from DNA fingerprints and repeated large-scale surveys.Crossref | GoogleScholarGoogle Scholar |
Van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M. D., and Shipley, P. (2004). MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535–538.
| MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXnvFOktb8%3D&md5=8f159c0b84827ce791b15209338a9746CAS |
Whitaker, K. (2006). Genetic evidence for mixed modes of reproduction in the coral Pocillopora damicornis and its effect on population structure. Marine Ecology Progress Series 306, 115–124.
| Genetic evidence for mixed modes of reproduction in the coral Pocillopora damicornis and its effect on population structure.Crossref | GoogleScholarGoogle Scholar |
Yasuda, N., Nagai, S., Hamaguchi, M., Okaji, K., Gerard, K., and Nadaoka, K. (2009). Gene flow of Acanthaster planci (L.) in relation to ocean currents revealed by microsatellite analysis. Molecular Ecology 18, 1574–1590.
| Gene flow of Acanthaster planci (L.) in relation to ocean currents revealed by microsatellite analysis.Crossref | GoogleScholarGoogle Scholar |
