Existence of microsatellites in expressed sequence tags of common carp (Cyprinus carpio L.) available in GenBank dbEST database
Common carp expressed sequence tags (ESTs) were analyzed for the existence of microsatellites, or simple sequence repeats (SSRs). In the NCBI dbEST database, a total of 10612 sequences were registered before December 31, 2004. A complete search of 2–6 nucleotide microsatellites resulted in the identification of 513 SSR-containing ESTs, accounting for 4.8% of the total. Cluster analysis indicated that 73 sequences of SSR-containing ESTs fell into 27 groups and the remaining 440 ESTs were indenpendent. A total of 467 unique SSR-containing ESTs were identified. These EST-SSRs contained a variety of simple sequence types, and di- and tri-nucleotide repeats were the most abundant, accounting for 42.1% and 27.9% of the whole, respectively. Of the dinucleotide repeats, CA/TG was the most abundant, followed by GA/TC. BLASTx search showed that 38.1% of the SSR loci could be associated with genes or proteins of known or unknown function. BLASTx searches of SSR-containing ESTs also showed high frequencies (98/179) of hits on zebrafish sequences.
Key wordscommon carp microsatellites ESTs data mining
Unable to display preview. Download preview PDF.
- Aliah, R. S., M. Takagi, S. Dong, C. T. Teoh, and N. Taniguchi, 1999. Isolation and inheritance of microsatellite markers in the common carpCyprinus carpio.Fish. Sci.,65: 235–239.Google Scholar
- Dietrich, W. F., J. L. Weber, D. A. Nickerson, and P. Kwok, 1998. Identification and analysis of DNA polymorphisms. In:Genome Analysis: A Laboratory Manual, Vol. 2: Detecting Genes. Birren, B.,et al., eds., Cold Spring Harbor Laboratory Press, New York, 494 pp.Google Scholar
- Garcia de Leon, F. J., J. F. Dallas, B. Chatain, M. Canonne, J. J. Versini,et al., 1995. Development and use of microsatellite markers in sea bassDicentrachus labrax (Linnaeus, 1758) (Percifirm: Serrandidae).Mol. Mar. Biol. Biotechnol.,4: 62–68.Google Scholar
- Nelson, J., 1994.Fishes of the World., Wiley, New York, USA, 600 pp.Google Scholar
- Powell, W., G. C. Machray, and J. Provan, 1996. Polymorphism revealed by simple sequence repeats.Trends Plant. Sci.,7: 215–222.Google Scholar
- Sun, X., Z. Jia, D. Wei, C. Lu, and L. Liang. 2005. Comparison between magnetic beads enriched and small inserted fragment library for microsatellite sequences of common carps.J. Fish. Sci. Chin.,12: 126–132.Google Scholar
- Wang, Z., J. L. Weber, G. Zhong, and S. D. Tanksley, 1994. Survey of plant short tandem DNA repeats.Theor. Appl. Genet.,88: 1–6.Google Scholar
- Wei, D., Y. Lou, X. Sun, and J., Shen, 2001. Isolation of microsatellite markers in the common carp (Cyprinus carpio).Zool. Res.,22: 238–241.Google Scholar