The regulatory network underlying gene expression divergence of gene duplicates in Atlantic salmon

Abstract

Atlantic salmon, provides excellent opportunities for studying vertebrate genome evolution after whole genome duplication (WGD). This remains congruent with the extreme rate of duplicated gene copies following Ss4R (fourth round of whole genome duplication) in the common ancestor of salmonids. However, little is known about the role of TFs in driving duplicate gene expression divergence. Here we aimed at contributing to the understanding of TF evolvability by modelling a TF gene regulatory network using the Inferelator algorithm for the first time in Atlantic salmon genome. This was achieved by using ATAC-seq data and RNA-Seq gene expression counts. With this network, we studied the tendency of TFs to evolve towards asymmetric expression of duplicate gene copies, where one copy diverted to expression gain leaving another copy retained, performing ancestral function. Firstly, our network analysis implied that Inferelator modelled a biologically meaningful network. Along with this, TF evolvability indicated, presence of conserved TFs, despite the expression dissimilarities between duplicates. Moreover, our gene ontology results suggested that these TFs were mostly involved in the cell cycle function. In conclusion, we suggest that modification in the co activators of our TFs could explain their being preserved towards asymmetric expression patterns of the duplicates.