Abstract
BackgroundTransposable elements 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 may have dramatic consequences on genome structure. Hybrid and polyploid clones have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the evolution of a DNA transposable element named Pokey in the D. pulex complex.ResultsPortions of Pokey elements inserted in the 28S rRNA genes from various Daphnia hybrids (diploids and polyploids) were sequenced and compared to sequences from a previous study to understand the evolutionary history of the elements. Pokey sequences show a complex phylogenetic pattern. We found evidence of recombination events in numerous Pokey alleles from diploid and polyploid hybrids and also from non-hybrid diploids. The recombination rate in Pokey elements is comparable to recombination rates previously estimated for 28S rRNA genes in the congener, Daphnia obtusa. Some recombinant Pokey alleles were encountered in Daphnia isolates from multiple locations and habitats.ConclusionsPhylogenetic and recombination analyses showed that recombination is a major force that shapes Pokey evolution. Based on Pokey phylogenies, reticulation has played and still plays an important role in shaping the diversity of the D. pulex complex. Horizontal transfer of Pokey seems to be rare and hybrids often possess Pokey elements derived from recombination among alleles encountered in the putative parental species. The insertion of Pokey in hotspots of recombination may have important impacts on the diversity and fitness of this transposable element.
Highlights
Transposable elements play a major role in genome evolution
Structure of the Pokey transposase gene Sequencing of RT-polymerase chain reaction (PCR) products, performed on RNA extracted from a sexual isolate of D. pulex (PX2-ON-9, Additional file 1), showed that a sequence upstream of the proposed stop codon in the 6.6 kb Pokey element is the beginning of a 68 bp canonical GT-AG intron
Recombination signals Forty-four sequences of the 3’ end of Pokey elements were added to nine Pokey alleles previously sequenced from non-hybrid isolates for a total of 53 sequences analyzed
Summary
Transposable elements 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 may have dramatic consequences on genome structure. Numerous studies have explored whether TE history reflects the evolutionary history of their hosts (that is, co-evolution [4,5,6,7]) Due to their high densities in eukaryotic genomes and their irreversible mode of insertion, some authors have proposed that SINEs (Short INterspersed Elements, non-autonomous Class I TEs) may be used for inferring the evolutionary. Diploid hybrids always have D. pulex mitochondrial genomes (mtDNA) and have been found to reproduce by obligate parthenogenesis in nature based on patterns of allozyme variation [18,26] and laboratory crosses [26], but see [27] for experimentally produced hybrids capable of sexual reproduction. Analyses of allozyme variation indicate that introgression is rare or nonexistent in areas where the two species co-occur [16,18,25] but a recent study using mitochondrial and nuclear markers has shown that introgression between these species had a substantial impact on their evolutionary history [28]
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