Gene duplication is an evolutionary mechanism providing new genetic material and opportunities to acquire new functions. After duplication, paralogs can encounter various fates. A large number is lost via pseudogenization due to the accumulation of deleterious mutations. However, a significant proportion is maintained through different paths (neo-functionalization, sub-functionalization and function redundancy).

To investigate how duplicated genes are maintained in the Drosophila melanogaster genome, we explored the function over-representation of all paralogs compared to singleton genes. We also considered the transposable element (TE) environment of genes. TEs are repeated sequences that can influence the expression of genes in their vicinity. They could thus influence the fate of duplicated genes. Our results show that both duplication status and the TE environment are associated with functional biases.

We also determined the expression divergence of pairs of duplicated genes and observed that it is associated to different factors like the age to duplication, the gene pairs localization and the TE neighborhood. In particular, the gene expression is more conserved when TEs are present in the vicinity of duplicated pair of genes compared to gene pairs devoid of TEs.

Our results allow to hypothesize that the presence of TEs near duplicated genes may be associated to their evolutionary fate.