Knowledge Management System of Northwest Institute of Plateau Biology, CAS
| Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing | |
| Wang, Jinjin1; Yu, Xiaomu; Zhao, Kai3; Zhang, Yaoguang1; Tong, Jingou; Peng, Zuogang1 | |
| 2012-03-01 | |
| 发表期刊 | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
 |
| ISSN | 1661-6596 |
| 卷号 | 13期号:3页码:3009-3021 |
| 文章类型 | Article |
| 摘要 | 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.; 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. |
| 关键词 | High-throughput Microsatellite Isolation Next-generation Sequencing Breams Cross-amplification |
| WOS标题词 | Science & Technology ; Physical Sciences |
| 关键词[WOS] | POLYMORPHIC MICROSATELLITES ; LOCI ; CARP ; TECHNOLOGY ; LIBRARIES ; SOFTWARE ; MARKERS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS研究方向 | Chemistry |
| WOS类目 | Chemistry, Multidisciplinary |
| WOS记录号 | WOS:000302174500031 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://210.75.249.4/handle/363003/3710 |
| 专题 | 中国科学院西北高原生物研究所 |
| 作者单位 | 1.Southwest Univ, Key Lab Aquat Sci Chongqing, Sch Life Sci, Key Lab Freshwater Fish Reprod & Dev,Minist Educ, Chongqing 400715, Peoples R China 2.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China 3.Chinese Acad Sci, NW Plateau Inst Biol, Key Lab Adaptat & Evolut Plateau Biota AEPB, Xining 810001, Peoples R China |
| 推荐引用方式 GB/T 7714 | Wang, Jinjin,Yu, Xiaomu,Zhao, Kai,et al. Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2012,13(3):3009-3021. |
| APA | 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.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,13(3),3009-3021. |
| MLA | Wang, Jinjin,et al."Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 13.3(2012):3009-3021. |
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