Abstract
BackgroundTransposable Elements (TEs) make up the majority of plant genomes, and thus understanding TE evolutionary dynamics is key to understanding plant genome evolution. Plant reproductive systems are diverse and mating type variation is one factor among many hypothesized to influence TE evolutionary dynamics. Here, we collected a large TE-display data set in self-fertilizing Arabidopsis thaliana, and compared it to data gathered in outcrossing Arabidopsis lyrata. We analyzed seven TE families in four natural populations of each species to tease apart the effects of mating system, demography, transposition, and selection in determining patterns of TE diversity.ResultsMeasures of TE band differentiation were largely consistent across TE families. However, patterns of diversity in A. thaliana Ac elements differed significantly from that other TEs, perhaps signaling a lack of recent transposition. Across TE families, we estimated higher allele frequencies and lower selection coefficients on A. thaliana TE insertions relative to A. lyrata TE insertions.ConclusionsThe differences in TE distributions between the two Arabidopsis species represents a synthesis of evolutionary forces that include the transposition dynamics of individual TE families and the demographic histories of populations. There are also species-specific differences that could be attributed to the effects of mating system, including higher overall allele frequencies in the selfing lineage and a greater proportion of among population TE diversity in the outcrossing lineage.
Highlights
Transposable Elements (TEs) make up the majority of plant genomes, and understanding TE evolutionary dynamics is key to understanding plant genome evolution
These empirical results are consistent with previous studies suggesting that some Basho subfamilies may be absent from A. lyrata [54]
The motivation for this study was to determine whether observed differences in the frequency and population dynamics of TEs can be attributed to species-wide effects, which presumably reflect differences between outcrossing and selfing mating systems, or are better attributed to factors like transposition dynamics and demographic history that may differ between species
Summary
Transposable Elements (TEs) make up the majority of plant genomes, and understanding TE evolutionary dynamics is key to understanding plant genome evolution. TEs can accrue rapidly after polyploid and hybrid speciation events [10,11] These observations raise questions about the evolutionary forces that govern the distribution of TEs within plant genomes. Population genetics has the potential to illuminate these forces, but our understanding of the population genetics of TEs has been based primarily on studies of Drosophila melanogaster These studies have revealed that there are far fewer TE insertions in the D. melanogaster genome than possible insertion sites [12,13] and that insertions tend to be at low population frequencies [12,13,14]. Another possibility is that TEs facilitate deleterious chromosome rearrangements through non-homologous (or ectopic) recombination [18,24,25,26,27,28]
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