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Open Access Short Report

Intragenic tandem repeats in Daphnia magna: structure, function and distribution

Isabelle Colson, Louis Du Pasquier and Dieter Ebert*

Author Affiliations

Basel University, Zoological Institute, Vesalgasse 1, CH-4051 Basel, Switzerland

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BMC Research Notes 2009, 2:206  doi:10.1186/1756-0500-2-206

Published: 6 October 2009

Abstract

Background

Expressed sequence tag (EST) databases provide a valuable source of genetic data in organisms whose genome sequence information is not yet compiled. We used a published EST database for the waterflea Daphnia magna (Crustacea:Cladocera) to isolate variable number of tandem repeat (VNTR) markers for linkage mapping, Quantitative Trait Loci (QTL), and functional studies.

Findings

Seventy-four polymorphic markers were isolated and characterised. Analyses of repeat structure, putative gene function and polymorphism indicated that intragenic tandem repeats are not distributed randomly in the mRNA sequences; instead, dinucleotides are more frequent in non-coding regions, whereas trinucleotides (and longer motifs involving multiple-of-three nucleotide repeats) are preferentially situated in coding regions. We also observed differential distribution of repeat motifs across putative genetic functions. This indicates differential selective constraints and possible functional significance of VNTR polymorphism in at least some genes.

Conclusion

Databases of VNTR markers situated in genes whose putative function can be inferred from homology searches will be a valuable resource for the genetic study of functional variation and selection.