Hellemans, B.

Klages, S.

Reinhart, R.

Souche, E.

Volckaert, F.A.M.J.

Open Marine Archive

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MINING FOR SINGLE NUCLEOTIDE POLYMORPHISMS IN EXPRESSED 
SEQUENCE TAGS OF SEA BASS 
Souche Erika1, Bart Hellemans1, Sven Klages2, Richard Reinhart2 and Filip Volckaert1  
1 Laboratory of Aquatic Ecology, Katholieke Universiteit Leuven 
Charles De Bériotstraat 32, B-3000 Leuven, Belgium 
E-mail: erika.souche@bio.kuleuven.be 
2 Max Planck Institute for Molecular Genetics 
Ihnestrasse 63-73, 14195 Berlin, Germany 
 
Marine Genomics Europe (MGE) is a European Network of Excellence for the 
implementation of high-throughput genomic approaches in the biology of marine 
organisms. Three different genomic aspects are addressed: functional, comparative and 
environmental genomics. European sea bass (Dicentrarchus labrax) is one of the model 
organisms studied within MGE. Sequencing of Expressed Sequence Tags (ESTs) from 14 
tissue cDNA libraries was carried out to support the different genomic research sections. 
The EST information can be used to assess various genomic characteristics, such as the 
discovery of genomic polymorphisms. 
This project aims at discovering computationally Single Nucleotide Polymorphisms 
(SNPs) by exploiting the redundancy within sequenced ESTs. Various bioinformatic tools 
allow the detection of potential SNPs. Multiple alignments (containing at least four 
overlapping sequences) are processed by an online software called SNPServer (Savage 
et al., 2005). Genotypes of a panel of 20 sea basses from two wild populations are 
used to validate the SNPs discovered in silico. Initial screening is performed by 
heteroduplex analysis (Davies et al., 2002). Since this quick technique does not give any 
information regarding the SNP type and position, sequencing of the polymorphic loci is 
subsequently required. 
Discovered SNPs can be used as population genomic markers. Population genomics 
involves the study of numerous loci or genome regions in order to understand the role 
of genetic variation across populations. A set of markers, preferably distributed 
throughout the whole sea bass genome, will be selected. Hundred individuals from 
natural populations will be screened for this set of markers. Neutral loci (loci not 
evolving directly in response to selection) will then be distinguished from outlier loci 
(genome locations that show behaviour or patterns of variation that are extremely 
divergent from the rest of the genome) (Luikart et al., 2003). Outlier loci will be further 
studied to give insight to evolution, selection and adaptative processes in natural sea 
bass populations.  
References 
Savage D., J. Batley, T. Erwin, E. Logan, C.G. Love, G.A.C. Lim, E. Mongin, G. Barker, G.C. 
Spangenberg and D. Edwards. 2005. SNPServer: a real-time SNP discovery tool. Nucleic 
Acids Research 3:493-495. 
  - 58 - 
Davies H., G.R. Bignell, C. Cox, P. Stephens, S. Edkins, S. Clegg, J. Teague, H. Woffendin, 
M.J. Garnett, W. Bottomley, N. Davis, E. Dicks, R. Ewing, Y. Floyd, K. Gray, S. Hall, R. 
Hawes, J. Hughes, V. Kosmidou, A. Menzies, C. Mould, A. Parker, C. Stevens, S. Watt, S. 
Hooper, R. Wilson, H. Jayatilake, B.A. Gusterson, C. Cooper, J. Shipley, D. Hargrave, K. 
Pritchard-Jones, N. Maitland, G. Chenevix-Trench, G.J. Riggins, D.D. Bigner, G. Palmieri, 
A. Cossu, A. Flanagan, A. Nicholson, J.W.C. Ho, S.Y. Leung, S.T. Yuen, B.L. Weber, H.F. 
Seigler, T.L. Darrow, H. Paterson, R. Marais, C.J. Marshall, R. Wooster, M.R. Stratton and 
P.A. Futreal. 2002. Mutations of the BRAF gene in human cancer. Nature 417:949-954. 
Luikart G., P.R. England, D. Tallmon, S. Jordan and P. Taberlet. 2003. The power and promise 
of population genomics: from genotyping to genome typing. Nature Reviews 4:981-994. 
 


Mining for single nucleotide polymorphisms in expressed sequence tags of sea bass

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