Isolation and Characterization of Microsatellite DNA Markers in the Deep-Sea Amphipod Paralicella tenuipes by Illumina MiSeq Sequencing

Heather Ritchie, Alan J Jamieson, Stuart B Piertney

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
11 Downloads (Pure)


Here we describe the development of 16 polymorphic microsatellite markers using an Illumina MiSeq sequencing approach in the deep-sea amphipod Paralicella tenuipes. A total of 25,577,844 DNA sequences were filtered for microsatellite motifs of which 197,873 sequences were identified. From these sequences 64 had sufficient flanking regions for primer design and 16 of these loci were polymorphic. Between five and 30 alleles were detected per locus, with an average of 13.63 alleles per locus, across a total of 120 individuals from five separate deep sea trenches from the Pacific Ocean. For the 16 loci, observed and expected heterozygosity values ranged from 0.116 to 0.414 and 0.422 to 0.820, respectively, with one locus displaying significant deviation from Hardy-Weinberg equilibrium. The microsatellite loci that have been isolated and described here are the first molecular markers developed for deep sea amphipods and will be invaluable for elucidating the genetic population structure and the extent of connectivity between deep ocean trenches.
Original languageEnglish
Pages (from-to)367-371
Number of pages5
JournalJournal of Heredity
Issue number4
Early online date24 Mar 2016
Publication statusPublished - Jul 2016

Bibliographical note


This work was supported by the HADEEP projects, funded by the Nippon Foundation, Japan (2009765188), the Natural Environmental Research Council, UK (NE/E007171/1) and the Total Foundation, France.


We acknowledge additional support from the Marine Alliance for Science and Technology for Scotland (MASTS) funded by the Scottish Funding Council (Ref: HR09011) and contributing institutions. We also acknowledge support from the Leverhulme Trust to SBP. Additional sea time was supported by NIWA’s ‘Impact of Resource Use on Vulnerable Deep-Sea Communities’ project (CO1_0906). We thank the chief scientists, crew, and company of the Japanese RV Hakuho-Maru (KH0703 and KH0803), the RV Tansei-Maru (KT-09-03), the RV Kairei (KR0716), the German FS Sonne (SO197 and SO 209), and the New Zealand RV Kaharoa (KAH0190, KAH1109, KAH1202, KAH1301, and KAH1310). From NIWA, we thank Malcolm Clark, Ashley Rowden, Kareen Schnabel, Sadie Mills for logistical support at the NIWA Invertebrate Collection. We also thank Fredrik Søreide from Promare, USA, for supply of the Puerto-Rico samples, and Niamh Kilgallen for amphipod identification.


  • deep-sea amphipod
  • hadal zone
  • population structure
  • Paralicella
  • microsatellite
  • high-throughput sequencing


Dive into the research topics of 'Isolation and Characterization of Microsatellite DNA Markers in the Deep-Sea Amphipod Paralicella tenuipes by Illumina MiSeq Sequencing'. Together they form a unique fingerprint.

Cite this