Abstract
BackgroundTransposable elements (TEs) play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes and dramatic consequences on genome structure. The population dynamics and distribution of TEs are influenced by their mode of transposition, the availability of niches in host genomes, and host population dynamics. Theories predict an increase in the number of TE insertions following hybridization or polyploidization. Evolution of TEs in hybrids and polyploids has mostly been studied in plants; few studies have examined the impacts of hybridization and/or polyploidization on TEs in animals. Hybrids and polyploids have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the effects of ploidy level on polymorphism and number of Pokey element insertions in diploid and polyploid hybrid isolates from the Daphnia pulex complex.ResultsThe polymorphism of Pokey insertion sites did not depend solely on either the ploidy level or the genetic background of their host; therefore, it may be the result of interactions between these parameters and other parameters such as Pokey activity, selection and/or drift. No significant effect of ploidy level was found on the number of Pokey insertions using TE display and qPCR. However, the load of Pokey insertion sites and the number of unique insertion sites were slightly (but not significantly) higher in polyploids than in diploids.ConclusionsThese results suggest a lack of increase in the number of Pokey insertions following polyploidization but higher availability of Pokey insertion sites in polyploids than in diploids. Compared to previous TE display and qPCR results, the load of Pokey insertions in hybrid diploids was higher than in non-hybrid sexual and asexual diploids, which suggests an increase in the density of Pokey insertions following hybridization.
Highlights
Transposable elements (TEs) play a major role in genome evolution
According to the principal coordinate analysis (PCoA) on the host genetic background, axis 2 differentiates the hybrids with D. pulex mitochondria from the D. middendorffiana sensu lato (Figure 1B); it is axis 1 that differentiates these isolates according the PCoA from Pokey profiles
The second cluster based on Pokey profiles contains diploid hybrids with D. pulex mitochondrial haplotypes, D. tenebrosa isolates, and polyploids with Polar D. pulicaria (PC3-MB-4 and PC3MB-5) or D. middendorffiana sensu stricto (MI3-MB-2) mitochondrial haplotypes
Summary
Transposable elements (TEs) play a major role in genome evolution Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes and dramatic consequences on genome structure. Our study examines the effects of ploidy level on polymorphism and number of Pokey element insertions in diploid and polyploid hybrid isolates from the Daphnia pulex complex. Hybridization and polyploidization, which play a significant role in the diversification of plants and animals [16,17,18], might have an impact on the load and insertion site polymorphism of TEs. Activation of TEs has been observed in hybrid genomes [19,20,21,22] (there are contradictory results in hybrid sunflowers [23]), and polyploidization may lead to an increase in the density of TE insertions [24,25], there are contradictory results in allopolyploid plants [26]. Studying the dynamics of TEs in hybrids and polyploids may provide insight on the evolution of their genomes and their propensity to adapt to various environments
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