Int. J. Mol. Sci. 2012, 13(3), 3009-3021; doi:10.3390/ijms13033009
Article

Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing

1email, 2email, 3email, 1email, 2,* email and 1,* email
Received: 9 February 2012; in revised form: 23 February 2012 / Accepted: 27 February 2012 / Published: 6 March 2012
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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
PDF Full-text Download PDF Full-Text [202 KB, uploaded 19 June 2014 04:13 CEST]

Export to BibTeX |
EndNote


MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.

Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert