  Background: Transposable elements (TEs) in eukaryote genomes are
quantitatively the main components affecting genome size, structure and
expression. The dynamics of their insertion and deletion depend on diverse
factors varying in strength and nature along the genome. We address here how TE
sequence evolution is affected by neighboring genes and the chromatin status
(euchromatin or heterochromatin) at their insertion site. Results: We estimated
ages of TE sequences in Arabidopsis thaliana, and found that they depend on the
distance to the nearest genes: TEs located close to genes are older than those
that are more distant. Consequently, TE sequences in heterochromatic regions,
which are gene-poor regions, are surprisingly younger and longer than that
elsewhere. Conclusions: We provide evidence for biased TE age distribution
close or near to genes. Interestingly, TE sequences in euchromatin and those in
heterochromatin evolve at different rates, and as a result, could explain that
TE sequences in heterochromatin tend to be younger and longer. Then, we revisit
models of TE sequence dynamics and point out differences for TE-rich genomes,
such as maize and wheat, compared to TE-poor genomes such as fly and A.
thaliana.
