The differential expression patterns of paralogs in response to stresses indicate expression and sequence divergences

Abstract Backgroud: Theoretically, paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments. However, functional divergences and expression differences have arisen due to selective pressures and evolutional stresses. A comprehensive investigation of the expression patterns of paralogous gene pairs in response to various stresses and a study of correlations between the expression levels and sequence divergences of the paralogs are needed. Results: In this study, we analyzed the expression patterns of paralogous genes under different types of stress and investigated the correlations between the expression levels and sequence divergences of the paralogs. Firstly, we analyzed the differential expression patterns of the paralogs under four different types of stress (drought, cold, infection, and herbivory) and classified them into three types according to their expression patterns. Secondly, we further analyzed the differential expression patterns under various degrees of stress and constructed the corresponding co-expression networks of differentially expressed paralogs and transcription factors. Thirdly, we investigated the correlations between the expression levels and sequence divergences of the paralogs and identified positive correlations between expression level and sequence divergence. With regard to the sequence divergence, we identified correlations between selective pressure and phylogenetic relationship. Conclusions: These results shed light on differential expression patterns of paralogs in response to environmental stresses and are helpful for understanding the relations between expression levels and sequences divergences.