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Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing
The Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Beibei, Chongqing 400715, China
The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
The Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Plateau Institute of Biology, The Chinese Academy of Sciences, Xining 810001, China
* Authors to whom correspondence should be addressed.
Received: 9 February 2012; in revised form: 23 February 2012 / Accepted: 27 February 2012 / Published: 6 March 2012
Abstract: Megalobrama pellegrini is an endemic fish species found in the upper Yangtze River basin in China. This species has become endangered due to the construction of the Three Gorges Dam and overfishing. However, the available genetic data for this species is limited. Here, we developed 26 polymorphic microsatellite markers from the M. pellegrini genome using next-generation sequencing techniques. A total of 257,497 raw reads were obtained from a quarter-plate run on 454 GS-FLX titanium platforms and 49,811 unique sequences were generated with an average length of 404 bp; 24,522 (49.2%) sequences contained microsatellite repeats. Of the 53 loci screened, 33 were amplified successfully and 26 were polymorphic. The genetic diversity in M. pellegrini was moderate, with an average of 3.08 alleles per locus, and the mean observed and expected heterozygosity were 0.47 and 0.51, respectively. In addition, we tested cross-species amplification for all 33 loci in four additional breams: M. amblycephala, M. skolkovii, M. terminalis, and Sinibrama wui. The cross-species amplification showed a significant high level of transferability (79%–97%), which might be due to their dramatically close genetic relationships. The polymorphic microsatellites developed in the current study will not only contribute to further conservation genetic studies and parentage analyses of this endangered species, but also facilitate future work on the other closely related species.
Keywords: high-throughput microsatellite isolation; next-generation sequencing; breams; cross-amplification
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Wang, J.; Yu, X.; Zhao, K.; Zhang, Y.; Tong, J.; Peng, Z. Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing. Int. J. Mol. Sci. 2012, 13, 3009-3021.
Wang J, Yu X, Zhao K, Zhang Y, Tong J, Peng Z. Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing. International Journal of Molecular Sciences. 2012; 13(3):3009-3021.
Wang, Jinjin; Yu, Xiaomu; Zhao, Kai; Zhang, Yaoguang; Tong, Jingou; Peng, Zuogang. 2012. "Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing." Int. J. Mol. Sci. 13, no. 3: 3009-3021.