He, FeiZhang, XuHu, Jin-YongTurck, FranziskaDong, XueGoebel, UlrikeBorevitz, Justinde Meaux, Juliette2015-12-130737-4038http://hdl.handle.net/1885/78168Transposable elements (TEs) are so abundant and variable that they count among the most important mutational sources in genomes. Nonetheless, little is known about the genetics of their variation in activity or silencing across closely related species. Here, we demonstrate that regulation of TE genes can differ dramatically between the two closely related Arabidopsis species A. thaliana and A. lyrata. In leaf and floral tissues of F1 interspecific hybrids, about 47% of TEs show allele-specific expression, with the A. lyrata copy being generally expressed at higher level. We confirm that TEs are generally expressed in A. lyrata but not in A. thaliana. Allele-specific differences in TE expression are associated with divergence in epigenetic modifications like DNA and histone methylation between species as well as with sequence divergence. Our data demonstrate that A. thaliana silences TEs much better than A. lyrata. For long terminal repeat retrotransposons, these differences are more pronounced for younger insertions. Interspecific differences in TE silencing may have a great impact on genome size changes.Keywords: allele; Arabidopsis; Arabidopsis lyrata; article; controlled study; DNA methylation; epigenetics; gene control; gene expression; gene silencing; genetic association; genetic variability; genome size; histone methylation; hybrid; nonhuman; nucleotide seque Arabidopsis; epigenetic modification; expression variation; interspecific cis-regulatory divergence; transposable elements201210.1093/molbev/msr2812016-02-24