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Isolation and characterization of microsatellite loci from three widespread tropical sea cucumbers of the genus Holothuria (Echinodermata, Holothuroidea), and cross-amplification among them

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Abstract

Holothuria (Microthele) fuscogilva (Cherbonnier, 1980), Holothuria sp. type “Pentard” and Holothuria (Microthele) nobilis (Selenka, 1867) are three tropical sea cucumber taxa that are heavily fished worldwide for the beche-de-mer trade market. In order to investigate the population genetic structure, diversity and connectivity of these taxa, 16, 19 and 25 microsatellite loci were isolated from H. fuscogilva, Holothuria sp. type “Pentard” and H. nobilis DNA libraries, respectively. These loci were tested on 94, 60 and eight individuals of the respective species, collected from the Seychelles. The number of alleles per locus ranged from 2 to 30. The observed heterozygosity ranged from 0.245 to 0.890 for H. fuscogilva and from 0.200 to 0.950 for Holothuria sp. type “Pentard”, while the expected heterozygosity ranged from 0.231 to 0.952 and from 0.504 to 0.951, respectively. Several loci were at Hardy–Weinberg equilibrium and linkage disequilibrium was detected in only three pairs of loci. Cross-amplification was also tested and almost all loci (49 over 60) were polymorphic for at least two of the three studied taxa, showing high transferability among them. These loci represent useful tools for assessing genetic diversity and population structure of these three taxa in fishery areas, and therefore providing relevant knowledge for resource management.

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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, 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.

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Authors and Affiliations

  1. UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Université de La Réunion, Faculté des Sciences et Technologies, 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

    Hélène Magalon

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  1. Nicolas Oury
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  2. Marc Léopold
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  3. Hélène Magalon
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Correspondence to Hélène Magalon.

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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.

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Accession Numbers

Primer sequences are deposited on GenBank with accession numbers from MK007156 to MK007215.

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Oury, N., Léopold, M. & Magalon, H. 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 (2019). https://doi.org/10.1007/s11033-019-04747-1

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