Cloning and Characterization of Microsatellite Loci in a Gorgonian Coral, Junceella juncea (Anthozoa; Octocorallia; Ellisellidae) and Its Application in Clonal Genotyping Shang-Yin Vanson Liu, 1 Chang-Feng Dai, 1 Tung-Yung Fan, 2 Hon-Tsen Yu 3 1 Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC 10617 2 National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, ROC 944 3 Institute of Zoology and Department of Life Science, National Taiwan University, Taipei, Taiwan, ROC 10617 Received: 25 September 2003 / Accepted: 3 February 2004 / Online publication: 11 March 2005 Abstract We attempted to isolate microsatellites from a Symbiodinium-free gorgonian octocoral, Junceella juncea, using two methods, partial genomic library screening and enrichment. Among the 3856 clones screened by the partial library method, 10 possibly positive signals were found, and 3 of them could be used to design primers and amplified consistently. In contrast, only one locus isolated by the enrich- ment method gave reliable amplification and was useful. The results indicate that microsatellites are rare in Junceella juncea, as reported for other cnidarians. Overall, we obtained 4 polymorphic loci to test the feasibility in investigating clonal struc- ture of J. juncea. A total of 40 multilocus genotypes were found among 152 colonies, and the number of genotypes (clones) identified at 7 reefs ranged from 2 to 16. The results of a nonmetric multidimen- sional scaling analysis indicated the recruitment of J. juncea populations mainly comes from self- retention. These novel microsatellite loci will pro- vide a useful tool to study clonal structure and population genetics for J. juncea in the future. Key words: Junceella — microsatellite — clonal struc- ture — coral Introduction Simple sequence repeats, or microsatellites, are tandem repeats of 1 to 6 nucleotides and are dis- tributed throughout the eukaryotic and prokaryotic genomes (Ashley and Dow, 1994). Unequal crossing over in meiosis and strand slippage replication are recognized as two major mechanisms for creating polymorphisms of microsatellites (Levinson and Gutman, 1987). Strand-slippage replication appears to be the predominant mode at microsatellites, and this slippage creates a loop that upon DNA repair would either be removed or lead to the elongation of the repeat. The high variances, the ability to distin- guish codominant alleles, Mendelian inheritance, and likely neutrality make it useful to study par- entage, population genetics, and conservation genetics (Goldstein and Schlo ¨ tterer, 1999). In Anthozoa, few microsatellite loci have been reported. One of the reasons is that most coral spe- cies contain algal endosymbionts (zooxanthellae), the DNA of which is easily mixed with coral DNA during conventional DNA extraction procedures. The algal DNA contamination makes it extremely difficult, if not impossible, to clone microsatellites from these corals unless some ‘‘decontamination’’ steps are used (Maier et al., 2001). The algal con- tamination does not pose a problem for the azoo- xanthellate coral, such as deep-sea coral Lophelia pertusa (Le Goff and Rogers, 2002), which does not contain endosymbiont algae. Nonetheless, after various approaches to clone microsatellite from corals were attempted by Ma ´ rquez et al. (2003), these authors concluded that in general microsatellite loci were scarce in coral genomes. Junceellam juncea Pallas, 1776 is an azooxan- thellate whip-like gorgonian coral distributed widely in Indo-Pacific reefs including New Guinea, Kei Is- land, Aru Island, Flores Sea, Banda Anchorage, Ti- mor, the Philippines, Australia, and Taiwan (Chen and Chang, 1991). Around Taiwan, J. juncea colonies Correspondence to: Hon-Tsen Yu; E-mail: ayu@ntu.edu.tw 26 DOI: 10.1007/s10126-004-0015-2  Volume 7, 26–32 (2005)  Ó Springer Science+Business Media, Inc. 2005