IHB OpenIR  > 鱼类生物学及渔业生物技术研究中心  > 期刊论文
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; Tong, JG (reprint author), Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China.
2012-03-01
Source PublicationINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN1661-6596
Volume13Issue:3Pages:3009-3021
AbstractMegalobrama 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.
SubtypeArticle
KeywordHigh-throughput Microsatellite Isolation Next-generation Sequencing Breams Cross-amplification
Department[Wang, Jinjin; Zhang, Yaoguang; Peng, Zuogang] Southwest Univ, Key Lab Aquat Sci Chongqing, Sch Life Sci, Key Lab Freshwater Fish Reprod & Dev,Minist Educ, Chongqing 400715, Peoples R China; Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China; [Zhao, Kai] Chinese Acad Sci, NW Plateau Inst Biol, Key Lab Adaptat & Evolut Plateau Biota AEPB, Xining 810001, Peoples R China
DOI10.3390/ijms13033009
WOS HeadingsScience & Technology ; Physical Sciences
Funding OrganizationNational Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045] ; National Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045] ; National Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045] ; National Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045]
Indexed BySCI
Language英语
WOS Research AreaChemistry
WOS SubjectChemistry, Multidisciplinary
WOS IDWOS:000302174500031
WOS KeywordPOLYMORPHIC MICROSATELLITES ; LOCI ; CARP ; TECHNOLOGY ; LIBRARIES ; SOFTWARE ; MARKERS
Funding OrganizationNational Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045] ; National Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045] ; National Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045] ; National Natural Science Foundation of China[30970341, 31071903]; Chongqing Natural Science Foundation (CSTC)[2010BB1015]; Fundamental Research Funds for the Central Universities[XDJK2011B010]; Special Fund for Agro-scientific Research in the Public Interest of China[200903048-08, 200903045]
Citation statistics
Cited Times:37[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/16949
Collection鱼类生物学及渔业生物技术研究中心_期刊论文
Corresponding AuthorTong, JG (reprint author), Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China.
Affiliation1.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
Recommended Citation
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.,...&Tong, JG .(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.
Files in This Item:
File Name/Size DocType Version Access License
Microsatellite Devel(202KB) 开放获取--View Application Full Text
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Wang, Jinjin]'s Articles
[Yu, Xiaomu]'s Articles
[Zhao, Kai]'s Articles
Baidu academic
Similar articles in Baidu academic
[Wang, Jinjin]'s Articles
[Yu, Xiaomu]'s Articles
[Zhao, Kai]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Wang, Jinjin]'s Articles
[Yu, Xiaomu]'s Articles
[Zhao, Kai]'s Articles
Terms of Use
No data!
Social Bookmark/Share
File name: Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing.pdf
Format: Adobe PDF
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.