Related Experiment Video
Updated: Jun 19, 2026

Resurrection of Dormant Daphnia magna: Protocol and Applications
Published on: January 19, 2018
Intragenic tandem repeats in Daphnia magna: structure, function and distribution
Isabelle Colson1, Louis Du Pasquier, Dieter Ebert
1Basel University, Zoological Institute, Vesalgasse 1, CH-4051 Basel, Switzerland. i.colson@bangor.ac.uk
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.
Related Concept Videos
Polytene Chromosomes
Exon Recombination
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Lampbrush Chromosomes
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops resemble the...
Position-effect Variegation
Gene Duplication and Divergence
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Non-LTR Retrotransposons

