The apple tribe is native to the Tian Shan mountains in Asia [1]. The common ancestor of apple and pear underwent a whole genome duplication (WGD) that occurred during Himalayan chain formation. This WGD, dated 27 Mya [2], resulted in autopolyploid plants containing two identical subgenomes [3]. Duplicated genes originating from WGD are named ohnologous genes [4]. This WGD is considered as a genomic shock, which associated with major environmental changes due to ground elevation, may have led to a burst of transposable elements (TE) 21 Mya [5]. We identified that QTLs in apple are not distributed evenly among ohnologous chro- mosomes. This imbalance has been associated with significant differences in the expression level of ohnologous genes in M. domestica [2].

Using 149 RNA-seq experiments derived from a wide array of apple cultivars, we performed differential expression analysis to compare ohnologous genes expression [2]. We identified 828 ohnologous gene pairs for which one gene of the pair was systematically overexpressed relative to the other in all experiments. We named these genes ”non switching”.

In this project we focus on non switching pairs and compare them to a random sample of 828 ohnologous pairs with differential expression level varying throughout the RNA-seq experiments (called swiching genes).

Our objective is to identify the epi/genetic mechanisms that may explain the observed differential expression within the non switching group. The TE environment of the genes were analyzed using TEGRIP pipeline [6], which extract the TE insertion's position relative to the genes. An enrichment analysis was then performed to associate particular TE environment(s) (including TE composition and insertion's locus) with each gene classes. The results will inform us on the evolution of TE environment post WGD, and whether TE insertion nearby genes causes differential expression among ohnologous pairs.