Isolation and characterisation of 14 novel microsatellite markers through Next Generation Sequencing for the commercial Atlantic seabob shrimp Xiphopenaeus kroyeri

  • Thomas R. H. KerkhoveEmail author
  • Bart Hellemans
  • Marleen De Troch
  • Annelies De Backer
  • Filip A. M. Volckaert
Short Communication


Assessing population genetic structure is a crucial step to support fisheries and conservation management. DNA microsatellite molecular markers are a widely used tool in population genotyping. In the present study, we characterised and developed 14 novel polymorphic microsatellite markers for a decapod crustacean, the Atlantic seabob shrimp Xiphopenaeus kroyeri (Heller, 1862), through rapid and cost-effective Illumina shotgun sequencing and a Galaxy-based bioinformatic pipeline. We genotyped 60 individuals from 2 populations with the newly developed microsatellites, resulting in the detection of 3 to 29 alleles per locus. Four loci deviated from Hardy–Weinberg equilibrium. Cross-amplification in a cryptic congeneric species was successful for eight loci (57%). The microsatellite loci developed in this study will be highly relevant for genetic and evolutionary studies of X. kroyeri, and for the stock management of this commercially exploited species.


Population structure Shotgun sequencing DNA microsatellites Decapoda Sustainable fisheries Western Atlantic 



We would like to thank Noble House Seafoods Limited, the Fisheries Department of the Ministry of Agriculture of Guyana, T. Willems of the Fisheries Department of the Ministry of Agriculture, Animal Husbandry and Fisheries of Suriname, S. Hall of Heiploeg Suriname and L. Baulier, M. Tagliarolo and F. Blanchard of Ifremer Guyane for supporting and assisting in the sample collection. We are grateful to J. Boyen for his assistance in the molecular analyses. We thank two anonymous reviewers for their helpful comments on a previous draft of the manuscript. This study was carried out with infrastructure funded by the European Marine Biological Resource Centre (EMBRC) Belgium – Research Foundation – Flanders (FWO) project (GOH3817N) and with an operational grant from the Flemish Interuniversity Council – Interuniversity Development Cooperation (VLIR-UOS) Global Minds Fund (GMF-OPR-32) from Ghent University awarded to T. Kerkhove and M. De Troch. The first author acknowledges a PhD scholarship from VLIR-UOS (VLADOC 2015-2019).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving animal and human participants

Not applicable.


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Marine Biology Research Group, Department of BiologyGhent UniversityGhentBelgium
  2. 2.Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
  3. 3.Animal Sciences, Aquatic Environment and Quality Research AreaFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)OstendBelgium

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