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Journal of Heredity Advance Access published online on November 28, 2008
Journal of Heredity, doi:10.1093/jhered/esn100
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© The American Genetic Association. 2008. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Microsatellite Characterization and Marker Development from Public EST and WGS Databases in the Reef-Building Coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia)

Shi Wang*, Lingling Zhang*, and Mikhail Matz

From the Section of Integrative Biology, School of Biological Sciences, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712

Address correspondence to S. Wang at the address above, or e-mail: swang{at}mail.utexas.edu.

Mining for microsatellites (also called simple sequence repeats [SSRs]) in public sequence databases of a common Indo-Pacific coral Acropora millepora identified 191 SSRs from 10 258 expressed sequence tag (EST) and 618 SSRs from 14 625 whole-genome shotgun (WGS) sequences. In contrast to other animals, trinucleotide repeats, rather than dinucleotide repeats, are dominant in the WGS-SSRs, and AAT is the most frequent trinucleotide motif in EST-SSRs. We successfully developed 40 polymorphic markers from EST-SSRs and WGS-SSRs. Both EST- and WGS-SSRs show high levels of polymorphism within corals from the same reef patch. Interestingly, markers WGS079 and WGS227 revealed SSR duplications in a few individuals, suggesting recent duplication events. Genotypic linkage disequilibrium was identified in 5 pairs of SSR markers, which will be invaluable for high-resolution studies of genetic admixture in natural populations of A. millepora. Transferability analysis showed that 25 of these markers can be successfully amplified in one of the most ubiquitous Indo-Pacific corals Acropora hyacinthus. The marker collection reported here is the largest ever developed for any reef-building coral. It holds great potential for addressing coral reef connectivity across the Indo-Pacific with an unprecedented precision, especially taking into account the cross-species transferability of a substantial number of markers.

Key Words: connectivity • genome mapping • linkage disequilibrium • locus duplication • population genetics • transferability

* These authors contributed equally to this work.

Corresponding Editor: Jose Lopez

Received July 24, 2008
Revised October 13, 2008
Accepted November 4, 2008


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