Research Article

New polymorphic microsatellite loci of threadsail filefish, Stephanolepis cirrhifer (Teleostei, Monacanthidae), from Korean waters

Published: May 14, 2013
Genet. Mol. Res. 12 (2) : 1679-1690 DOI: 10.4238/2013.May.14.8

Abstract

The threadsail filefish, Stephanolepis cirrhifer (Monacanthidae), is found mainly in the western Pacific. It is intensively caught in Korea and is a highly appreciated seafood delicacy. Consequently, the natural population of this species has drastically decreased, despite introductions from hatcheries. To provide information necessary for its conservation and management, we developed 24 polymorphic microsatellite markers using a combination of a total enriched genomic library and a small-scale 454 pyrosequencing. A total of 90,847 raw reads were obtained, and 75,128 unique sequences were generated, with an average length of 477 bp; 5350 (7.12%) sequences contained a minimum of 5 di- to tetranucleotide repeat motifs. Seventy-four sequences were used for microsatellite primer design. They all amplified successfully; 24 were polymorphic, with 8 containing trinucleotide repeats and 3 containing tetranucleotide repeats. The genetic variations based on 15 primer sets were investigated using 45 wild individuals from the coastal waters of Geomun Island. The number of alleles per locus varied from 4 to 15, with an average of 7.47. The observed and expected heterozygosities ranged from 0.333 to 0.956 and from 0.316 to 0.870, with averages of 0.692 and 0.701, respectively. No linkage disequilibrium was found between any pair of loci, indicating their independence. One locus significantly deviated from Hardy-Weinberg equilibrium after Bonferroni’s correction; this may be due to the existence of a null allele. Cross-amplification was also tested for all 24 polymorphic loci in another monacanthid species, Thamnaconus modestus; 7 loci were effectively amplified. The high degree of polymorphism that was exhibited by the 15 newly developed microsatellites will be useful for assessing genetic variation and for conservation genetic studies of these 2 monacanthid species.

The threadsail filefish, Stephanolepis cirrhifer (Monacanthidae), is found mainly in the western Pacific. It is intensively caught in Korea and is a highly appreciated seafood delicacy. Consequently, the natural population of this species has drastically decreased, despite introductions from hatcheries. To provide information necessary for its conservation and management, we developed 24 polymorphic microsatellite markers using a combination of a total enriched genomic library and a small-scale 454 pyrosequencing. A total of 90,847 raw reads were obtained, and 75,128 unique sequences were generated, with an average length of 477 bp; 5350 (7.12%) sequences contained a minimum of 5 di- to tetranucleotide repeat motifs. Seventy-four sequences were used for microsatellite primer design. They all amplified successfully; 24 were polymorphic, with 8 containing trinucleotide repeats and 3 containing tetranucleotide repeats. The genetic variations based on 15 primer sets were investigated using 45 wild individuals from the coastal waters of Geomun Island. The number of alleles per locus varied from 4 to 15, with an average of 7.47. The observed and expected heterozygosities ranged from 0.333 to 0.956 and from 0.316 to 0.870, with averages of 0.692 and 0.701, respectively. No linkage disequilibrium was found between any pair of loci, indicating their independence. One locus significantly deviated from Hardy-Weinberg equilibrium after Bonferroni’s correction; this may be due to the existence of a null allele. Cross-amplification was also tested for all 24 polymorphic loci in another monacanthid species, Thamnaconus modestus; 7 loci were effectively amplified. The high degree of polymorphism that was exhibited by the 15 newly developed microsatellites will be useful for assessing genetic variation and for conservation genetic studies of these 2 monacanthid species.

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