Zoological Studies

Vol. 57, 2018

(update: 2018.06.12) 

Development of Novel Polymorphic Microsatellite Markers in Catch Bowl Coral, Isopora palifera (Scleractinia; Acroporidae) Using Next-generation Sequencing

Sung-Yin Yang1, Wai-Ling Fong1,2, Wenhua Savanna Chow1,3,4, Chia-Min Hsu1,2, Chia-Ling Carynn Chan1, Shashank Keshavmurthy1,*, and Chaolun Allen Chen1,2,3,4,*

1Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: likefh@gmail.com (Yang); christine29632003@gmail.com (Fong); savanna.201@gmail.com (Chow); chiamean@gmail.com (Hsu); carynnchan84@gmail.com (CC Chan)
2Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
3Deparment of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
4Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Nankang, Taipei 115, Taiwan

(Received 23 March 2018; Accepted 21 May 2018; Communicated by Benny K.K. Chan)

Sung-Yin Yang, Wai-Ling Fong, Wenhua Savanna Chow, Chia-Min Hsu, Chia-Ling Carynn Chan, Shashank Keshavmurthy, and Chaolun Allen Chen (2018) Catch bowl coral, Isopora palifera, is a shallow-water scleractinian species distributed in the Indo-West Pacific region, and has been studied for its reproduction, symbiont diversity, and population genetics. In order to develop microsatellite markers to reveal the genetic connectivity of I. palifera in the Kenting reefs, southern Taiwan, we applied a stepwise approach including Illumina sequencing, primer screening, and validation. DNA sequences of each 6,363,035 read pairs were assembled with high coverage and sequencing depth, and 1,173,835 potential SSRs were identified. A set of 60,986 primers were designed and tested, and six novel microsatellite markers with three type motifs, including 3 di- and 3 tetra- repeats, were successfully isolated. The ranges in number of alleles per locus and observed and expected heterozygosities were 3-5, 0.444-0.538, and 0.375-0.565, respectively. Application of these loci to the genetic diversity of an I. palifera population that experienced bleaching events in the Kenting reef between 1998 and 2015 showed a signature admixture of three clusters without temporal variation. These loci are useful for studying population genetics in the genus Isopora. Our results suggest that next-generation sequencing technology is convenient and cost-effective and can be utilized to isolate microsatellites in other reef-building corals.

Key words: Isopora palifera, Coral, Microsatellites, Next-generation sequencing.

*Correspondence: CA Chen and S Keshavmurthy contributed equally to this work. Tel: 886-2-2789-9549. Fax: 886-2-2789-9624. E-mail: cac@gate.sinica.edu.tw (Chan); shashank@gate.sinica.edu.tw (Keshavmurthy)