Abstract
BackgroundTheoretically, 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 throughout evolution. 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.ResultsIn 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. 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 main types according to their expression patterns. We then further analyzed the differential expression patterns under various degrees of stress and constructed corresponding co-expression networks of differentially expressed paralogs and transcription factors. Finally, 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 sequence divergence, we identified correlations between selective pressures and phylogenetic relationships.ConclusionsThese results shed light on differential expression patterns of paralogs in response to environmental stresses and are helpful for understanding the relationships between expression levels and sequences divergences.
Highlights
Paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments
Homolog identification and paralog expression classification We identified 6481 paralogs in the model plant species Arabidopsis thaliana based on a homology analysis which involved 20 other species using the InParanoid 8 Software [28]
The repeats of Arabidopsis thaliana were identified using the RepeatMasker and HashRepeatFinder tools. These results indicated that the paralogs and repeats were highly coincident with regard to their locations and interactions, and the corresponding coincidence rate was 82.4%. This which further confirmed that the paralogous gene pairs were mostly generated through genome duplications, including whole genome duplication (WGD) and small-scale duplications (SSDs) [2, 30]
Summary
Paralogous genes generated through whole genome duplications should share identical expression levels due to their identical sequences and chromatin environments. Functional divergences and expression differences have arisen due to selective pressures throughout evolution. Lian et al BMC Plant Biology (2020) 20:277 genes generated through WGDs should initially share identical sequences and chromatin environments and possess stronger expression correlations than would be found among other duplication types [12]. Paralogs should share identical expression levels in the absence of selective pressures and stress [13], because they share identical sequences. Functional divergences and expression differences have arisen due to selective pressures and harsh environments after hundreds of millions of years of evolution [14]. Gene expression divergence is an important evolutionary driving force for paralogs
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