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

doi:10.1093/jhered/esw019

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

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Abstract

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 language	English
Pages (from-to)	367-371
Number of pages	5
Journal	Journal of Heredity
Volume	107
Issue number	4
Early online date	24 Mar 2016
DOIs	https://doi.org/10.1093/jhered/esw019
Publication status	Published - Jul 2016

Bibliographical note

Funding

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.

Acknowledgments

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.

Keywords

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

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This is a pre-copyedited, author-produced PDF of an article accepted for publication in Journal of Heredity following peer review. The version of record J Hered (2016) 107 (4): 367-371. is available online at: doi: 10.1093/jhered/esw019
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Cite this

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

abstract = "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.",

keywords = "deep-sea amphipod, hadal zone, population structure, Paralicella, microsatellite, high-throughput sequencing",

author = "Heather Ritchie and Jamieson, {Alan J} and Piertney, {Stuart B}",

note = "Funding 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. Acknowledgments 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{\textquoteright}s {\textquoteleft}Impact of Resource Use on Vulnerable Deep-Sea Communities{\textquoteright} 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 S{\o}reide from Promare, USA, for supply of the Puerto-Rico samples, and Niamh Kilgallen for amphipod identification.",

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T1 - Isolation and Characterization of Microsatellite DNA Markers in the Deep-Sea Amphipod Paralicella tenuipes by Illumina MiSeq Sequencing

AU - Ritchie, Heather

AU - Jamieson, Alan J

AU - Piertney, Stuart B

N1 - Funding 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. Acknowledgments 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.

PY - 2016/7

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N2 - 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.

AB - 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.

KW - deep-sea amphipod

KW - hadal zone

KW - population structure

KW - Paralicella

KW - microsatellite

KW - high-throughput sequencing

U2 - 10.1093/jhered/esw019

DO - 10.1093/jhered/esw019

M3 - Article

SN - 0022-1503

VL - 107

SP - 367

EP - 371

JO - Journal of Heredity

JF - Journal of Heredity

IS - 4

ER -

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

Abstract

Bibliographical note

Keywords

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