%0 Journal Article
%T Intragenic tandem repeats in Daphnia magna: structure, function and distribution
%A Isabelle Colson
%A Louis Du Pasquier
%A Dieter Ebert
%J BMC Research Notes
%D 2009
%I BioMed Central
%R 10.1186/1756-0500-2-206
%X 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.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.Waterfleas of the genus Daphnia (Crustacea:Cladocera) are small planktonic crustaceans found in standing freshwater bodies around the world. They have a long history as model organisms for evolutionary, ecological and ecotoxicological research. Recently, the genus has been the focus of a major sequencing effort, and the full genome sequence of Daphnia pulex is now available [1]. Genomic resources are steadily being developed for another species of the genus, D. magna. In particular, a database of around 12,000 expressed sequence tags (EST) is currently available [1,2], providing a useful resource to isolate polymorphic genetic markers in this species. Developing genetic markers from transcribed sequences offers specific advantages compared to traditional methods of screening enriched genomic libraries. Apart from the lower cost and higher speed of development, EST-derived genetic markers have a higher probability of being functionally significant and of being located in gene-rich regions [3-5]. This makes them highly useful markers for QTL mapping of ecologically-relevant phenotypes and for the study of selection in natural populat
%U http://www.biomedcentral.com/1756-0500/2/206