Technology Report ARTICLE

Front. Mar. Sci., 23 May 2014 | http://dx.doi.org/10.3389/fmars.2014.00011

Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology

Chuya Shinzato1*, Yuki Yasuoka1, Sutada Mungpakdee1, Nana Arakaki2, Manabu Fujie2, Yuichi Nakajima3 and Nori Satoh1*
  • 1Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
  • 2DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
  • 3Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan

The genus Acropora (Scleractinia, Acroporidae) is one of the most widespread coral genera, comprising the largest number of extant species among scleractinian (reef-building) corals. Molecular phylogenetic studies have suggested that A. tenuis belongs to the most basal clade (clade I) while A. digitifera belongs to a derived clade (clade IV). In order to develop microsatellite markers that would be useful for most Acropora species, we sequenced the genomic DNA of A. tenuis, using a next generation sequencer (Illumina MiSeq), and designed primer sets that amplify microsatellite loci. Afterward we selected primer pairs with perfectly matched nucleotide sequences from which at least one primer was uniquely mapped to the A. digitifera genome. Fourteen microsatellite markers showed non-significant departure from Hardy–Weinberg equilibrium (HWE) in both A. tenuis and A. digitifera. Thus these markers could be used for wide range of species and may provide powerful tools for population genetics studies and conservation of Acropora corals.

Keywords: scleractinian coral, Acropora, microsatellite, population genetics, cross-species, Illumina next-generation sequencing

Citation: Shinzato C, Yasuoka Y, Mungpakdee S, Arakaki N, Fujie M, Nakajima Y and Satoh N (2014) Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology. Front. Mar. Sci. 1:11. doi: 10.3389/fmars.2014.00011

Received: 04 March 2014; Accepted: 08 May 2014;
Published online: 23 May 2014.

Edited by:

Irene Wagner-Doebler, Helmholtz Centre for Infection Research, Germany

Reviewed by:

Carmelo Fruciano, University of Konstanz, Germany
Susanna López-Legentil, University of North Carolina Wilmington, USA

Copyright © 2014 Shinzato, Yasuoka, Mungpakdee, Arakaki, Fujie, Nakajima and Satoh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Chuya Shinzato and Nori Satoh, 1919-1, Tancha, Onna, Okinawa, Japan e-mail: c.shinzato@oist.jp; norisky@oist.jp