Vol. 57, 2018
(update: 2018.06.12; 07.02)
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,*
Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail:
email@example.com (Yang); firstname.lastname@example.org (Fong);
email@example.com (Chow); firstname.lastname@example.org (Hsu);
email@example.com (CC Chan)
(Received 23 March 2018; Accepted 21 May
2018; Communicated by Benny K.K. Chan)
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.
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:
firstname.lastname@example.org (Chan); email@example.com