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New polymorphic microsatellite loci revealed for the dusky shark Carcharhinus obscurus through Ion Proton double-digest RAD sequencing

  • Simo N. Maduna
  • Charné Rossouw
  • Ruhan Slabbert
  • Sabine P. Wintner
  • Charlene da Silva
  • Aletta E. Bester-van der Merwe
Short Communication

Abstract

The non-model shark species, dusky shark Carcharhinus obscurus, is a bio-economically and recreationally important shark in many areas of its range. Despite of the fishery importance of C. obscurus few genetic resources are currently available for the species. Here, we report on the isolation of eight novel microsatellite loci from C. obscurus using a double-digest restriction site associated DNA (RAD) sequencing approach on the Ion Proton semiconductor platform (ddRADseq-ion). We characterised the loci in 26 individuals and all loci were polymorphic, exhibiting 5–10 alleles (average 6.6), and observed and expected heterozygosities of 0.385–0.962 and 0.479–0.847, respectively. We found that all pairs of loci were in linkage equilibrium and conformed to Hardy–Weinberg expectations. The loci reported in this study are only the second set of microsatellite loci ever characterized for C. obscurus and will be valuable for molecular ecology studies for this vulnerable species.

Keywords

Carcharhinus obscurus Double-digest Dusky shark Ion Proton Ion Torrent Microsatellites Population genetics RAD sequencing 

Notes

Acknowledgements

The financial assistance of the National Research Foundation (NRF) of South Africa towards this research is hereby acknowledged. Opinions expressed and conclusions arrived at, are those of the authors and are not necessarily to be attributed to the NRF.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Informed consent

No required for our submission.

Research involving human participants and/or animals

Sharks were collected by field scientist according to protocols and research permit (RES2014/01) approved by the Department of Agriculture, Forestry and Fisheries (DAFF), South Africa. The sampling strategies implemented in our study complied with the Convention on the Trade in Endangered Species of Wild Fauna and Flora (http://www.cites.org/).

Supplementary material

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Supplementary material 1 (XLSX 68 KB)
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Supplementary material 2 (XLSX 18 KB)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Molecular Breeding and Biodiversity Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
  2. 2.Roche Sequencing Solutions Cape TownCape TownSouth Africa
  3. 3.KwaZulu-Natal Sharks BoardUmhlanga RocksSouth Africa
  4. 4.School of Life SciencesUniversity of KwaZulu-NatalDurbanSouth Africa
  5. 5.Fisheries Research, Department of Agriculture, Forestry and FisheriesRogge BaySouth Africa
  6. 6.Department of Biological SciencesUniversity of Cape TownCape TownSouth Africa
  7. 7.Norwegian Institute of Bioeconomy ResearchNIBIO - SvanhovdSvanvikNorway

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