Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

Authors

Laura Taillebois, Charles Darwin University, Northern Territory
Christine Dudgeon, The University of Queensland, Australia
Safia Maher, The University of Queensland, Australia
David Crook, Charles Darwin University, Australia
Thor Saunders, Northern Territory Department of Primary Industry and Fisheries, Australia
Diane P. Barton, Charles Darwin University, Northern Territory
Jonathan A. Taylor, Department of Primary Industry and Resources, Northern Territory
David J. Welch, C2O Fisheries, Cairns, Queensland
Stephen J. Newman, Department of Fisheries, Western AustraliaFollow
Michael J. Travers, Department of Fisheries, Western AustraliaFollow
Richard J. Saunders, Centre for Sustainable Tropical Fisheries and Aquaculture, Townsville, Queensland,
Jennifer Ovenden, The University of Queensland, Australia

Document Type

Article

Publication Date

8-31-2016

Journal Title

PeerJ

ISSN

ISSN: 2167-8359

Keywords

Next-generation sequencing, Lutjanus johnii, Protonibea diacanthus, Multiplex panels, Microsatellite markers, Lethrinus laticaudis

Disciplines

Aquaculture and Fisheries | Genetics | Genomics | Marine Biology

Abstract

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

Recommended Citation

Taillebois L, Dudgeon C, Maher S, Crook DA, Saunders TM, Barton DP, Taylor JA, Welch DJ, Newman SJ, Travers MJ, Saunders RJ, Ovenden J. 2016. Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification. PeerJ 4:e2418 https://doi.org/10.7717/peerj.2418