Skip to main content
SpringerLink
Log in

Isolation and characterization of 42 microsatellite loci from the prickly redfish Thelenota ananas (Echinodermata, Stichopodidae)

  • Short Communication
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

The prickly redfish Thelenota ananas (Jaeger, 1833) is a widely distributed tropical sea cucumber. Populations of this species have been increasingly harvested throughout its distribution area in the Indo-Pacific region, which led to significant overexploitation issues. In order to investigate the genetic structure, diversity and connectivity of its populations, 42 microsatellite loci were isolated from a T. ananas microsatellite-enriched DNA library. These loci were characterized on 24 individuals collected from the Seychelles. The number of alleles per locus ranged from 3 to 22. The observed heterozygosity ranged from 0.083 to 0.952, while the expected heterozygosity ranged from 0.162 to 0.974. No linkage disequilibrium was detected among all loci and 20 loci (48%) were at Hardy–Weinberg equilibrium. These 42 loci represent useful tools for assessing genetic diversity, structure and gene flow among T. ananas populations, providing relevant knowledge for the management and conservation of those major commercial resources.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  1. Purcell SW, Mercier A, Conand C et al (2013) Sea cucumber fisheries: global analysis of stocks, management measures and drivers of overfishing. Fish Fish 14:34–59. https://doi.org/10.1111/j.1467-2979.2011.00443.x

    Article  Google Scholar 

  2. Anderson SC, Flemming JM, Watson R, Lotze HK (2011) Serial exploitation of global sea cucumber fisheries. Fish Fish 12:317–339. https://doi.org/10.1111/j.1467-2979.2010.00397.x

    Article  Google Scholar 

  3. Uthicke S, Benzie J (2001) Effect of bêche-de-mer fishing on densities and size structure of Holothuria nobilis (Echinodermata: Holothuroidea) populations on the Great Barrier Reef. Coral Reefs 19:271–276. https://doi.org/10.1007/s003380000118

    Article  Google Scholar 

  4. Bruckner AW, Johnson KA, Field JD (2003) Conservation strategies for sea cucumbers: Can a CITES Appendix II listing promote sustainable international trade. SPC Beche-de-Mer Inf Bull 18:24–33

    Google Scholar 

  5. Uthicke S, Welch D, Benzie JAH (2004) Slow growth and lack of recovery in overfished holothurians on the Great Barrier Reef: evidence from DNA fingerprints and repeated large-scale surveys. Conserv Biol 18:1395–1404. https://doi.org/10.1111/j.1523-1739.2004.00309.x

    Article  Google Scholar 

  6. Conand C (2008) Population status, fisheries and trade of sea cucumbers in Africa and the Indian Ocean. In: Toral-Granda V, Lovatelli A, Vasconcellos M (eds) Sea cucumbers: a global review of fisheries and trade, FAO Fisheries and Aquaculture Technical Paper No. 516. Food and Agriculture Organization, Rome, pp 143–193

    Google Scholar 

  7. Kinch U, Purcell S, Uthicke S, Friedman K (2008) Population status, fisheries and trade of sea cucumbers in the Western Central Pacific. In: Toral-Granda V, Lovatelli A, Vasconcellos M (eds) Sea cucumbers: a global review of fisheries and trade, FAO Fisheries and Aquaculture Technical Paper No. 516. Food and Agriculture Organization, Rome, pp 7–55

    Google Scholar 

  8. Choo PS (2008) Population status, fisheries and trade of sea cucumbers in Asia. In: Toral-Granda V, Lovatelli A, Vasconcellos M (eds) Sea cucumbers: a global review of fisheries and trade, FAO Fisheries and Aquaculture Technical Paper No. 516. Food and Agriculture Organization, Rome, pp 81–117

    Google Scholar 

  9. Kalaeb T, Ghirmay D, Semere Y, Yohannes F (2008) Status and preliminary assessment of the sea cucumber fishery in Eritrea. SPC Beche-de-Mer Inf Bull 27:8–12

    Google Scholar 

  10. Purcell SW, Samyn Y, Conand C (2012) Commercially important sea cucumbers of the world, FAO species catalogue for fishery purposes No. 6. Food and Agriculture Organization, Rome

    Google Scholar 

  11. Conand C, Gamboa R, Purcell S (2013) Thelenota ananas. IUCN Red List of Threatened Species e.T180481A1636021. https://doi.org/10.2305/IUCN.UK.2013-1.RLTS.T180481A1636021.en

  12. Purcell SW, Polidoro BA, Hamel J-F et al (2014) The cost of being valuable: predictors of extinction risk in marine invertebrates exploited as luxury seafood. Proc R Soc B 281:20133296. https://doi.org/10.1098/rspb.2013.3296

    Article  PubMed  PubMed Central  Google Scholar 

  13. Friedman K, Eriksson H, Tardy E, Pakoa K (2011) Management of sea cucumber stocks: patterns of vulnerability and recovery of sea cucumber stocks impacted by fishing. Fish Fish 12:75–93. https://doi.org/10.1111/j.1467-2979.2010.00384.x

    Article  Google Scholar 

  14. Léopold M, Thébaud O, Charles A (2019) The dynamics of institutional innovation: crafting co-management in small-scale fisheries through action research. J Environ Manag 237:187–199. https://doi.org/10.1016/j.jenvman.2019.01.112

    Article  Google Scholar 

  15. Meglécz E, Pech N, Gilles A et al (2014) QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate. Mol Ecol Resour 14:1302–1313. https://doi.org/10.1111/1755-0998.12271

    Article  CAS  PubMed  Google Scholar 

  16. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234. https://doi.org/10.1038/72708

    Article  CAS  PubMed  Google Scholar 

  17. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices version 2.9.3.2, updated from Goudet 1995

  19. Raymond M, Rousset F (1995) GenePop: population genetics software for exact tests and ecumenism. J Hered 86:248–249. https://doi.org/10.1111/j.1558-5646.1995.tb04456.x

    Article  Google Scholar 

  20. Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106. https://doi.org/10.1111/j.1471-8286.2007.01931.x

    Article  PubMed  Google Scholar 

  21. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300

    Google Scholar 

  22. van Oosterhout C, Hutchinson WF, Wills DP, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x

    Article  CAS  Google Scholar 

  23. Taquet C, Nagai S, Yasuda N, Nadaoka K (2011) First report of the development of microsatellite markers for a tropical sea cucumber (Stichopus chloronotus). Conserv Genet Resour 3:201–203. https://doi.org/10.1007/s12686-010-9322-2

    Article  Google Scholar 

  24. Chávez JMO, Portilla MÁDR, Aguilera LEC, Olivares AR (2018) Genetic connectivity of the endangered brown sea cucumber Isostichopus fuscus in the northern Gulf of California revealed by novel microsatellite markers. Rev Mex Biodivers 89:563–567. https://doi.org/10.22201/ib.20078706e.2018.2.2294

    Article  Google Scholar 

  25. Oury N, Léopold M, Magalon H (2019) Isolation and characterization of microsatellite loci from three widespread tropical sea cucumbers of the genus Holothuria (Echinodermata, Holothuroidea), and cross-amplification among them. Mol Biol Rep 46:3501–3510. https://doi.org/10.1007/s11033-019-04747-1

    Article  CAS  PubMed  Google Scholar 

  26. Fitch AJ, Leeworthy G, Li X et al (2013) Isolation and characterisation of eighteen microsatellite markers from the sea cucumber Holothuria scabra (Echinodermata: Holothuriidae). Aust J Zool 60:368–371. https://doi.org/10.1071/ZO12114

    Article  Google Scholar 

  27. Dailianis T, Tsigenopoulos CS, Dounas C, 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. Mol Ecol 20:3757–3772. https://doi.org/10.1111/j.1365-294X.2011.05222.x

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was conducted through a Grant of the SEACUSEY Collaborative Research Project (support for adaptive co-management of the SEA CUcumber fishery in SEYchelles; http://seacusey.ird.nc) as part of the “Coastal, Marine and Island Specific Biodiversity Management in ESA-IO Coastal States program” funded by the European Union and implemented by the Indian Ocean Commission. We thank the Seychelles Fishing Authority (SFA) including the Staff of R/V L’Amitié, Julie Caquelard, Ameer Ebrahim, Rodney Govinden and the voluntary professional skippers and divers for their assistance in data collection. We thank the Plateforme Gentyane of the Institut National de la Recherche Agronomique (INRA, Clermont-Ferrand, France) for genotyping and technical support.

Author information

Authors and Affiliations

  1. UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Faculté des Sciences et Technologies, Université de La Réunion, 15 Bd René Cassin, CS 92003, 97744, St Denis Cedex 09, La Réunion, France

    Nicolas Oury & Hélène Magalon

  2. UMR ENTROPIE (IRD, Université de La Réunion, CNRS), c/o IH.SM, University of Toliara, BP 141, Toliara, Madagascar

    Marc Léopold

  3. Laboratoire d’Excellence CORAIL, Perpignan, France

    Marc Léopold & Hélène Magalon

Authors
  1. Nicolas Oury
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marc Léopold
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hélène Magalon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hélène Magalon.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

Samples were collected on fished specimens only. Sampling and export permits of genetic samples were delivered by the SFA as part of a Collaborative Research Contract signed with the IRD on July, 24th 2017.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Accession Numbers: Primer sequences were deposited on GenBank with accession numbers from MK007216 to MK007250 and from MK723844 to MK723849.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 18 kb)

Supplementary material 2 (PDF 34 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Oury, N., Léopold, M. & Magalon, H. Isolation and characterization of 42 microsatellite loci from the prickly redfish Thelenota ananas (Echinodermata, Stichopodidae). Mol Biol Rep 46, 5569–5574 (2019). https://doi.org/10.1007/s11033-019-04957-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-019-04957-7

Keywords

Search

Navigation