Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana

Abstract

BackgroundWhole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown.ResultsHere, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3′ untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses.ConclusionsLoss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2803-2) contains supplementary material, which is available to authorized users.

Differential paralog divergence modulates genome evolution across yeast species

“…Many studies have aimed to determine whether adaptation and phenotypic change typically occur from mutations in non-coding or coding regions in the genome [ 51 – 55 ]. In the case of gene duplicates, it has been proposed that their retention provides genetic redundancy, buffering the mutational space to either acquire new function, or to partition the ancestral function between duplicates.…”

Evolution and functional differentiation of recently diverged phytochelatin synthase genes from Arundo donax L.

“…Moudouma et al , 2012; Yamazaki et al , 2018), the ancestral PCS existing before both duplications may have been up-regulated by Cd stress, like the present-day AdPCS1 and AdPCS2 genes; thus, we propose that the PCS B ancestral copy underwent subfunctionalization of regulatory promoter elements after divergence. This scenario is corroborated by the fact that stress-responsive genes tend to be over-represented among paralogous pairs with different expression levels and reduced conservation of cis -acting regulatory elements (Hoffmann and Palmgren, 2016). Interestingly, transcriptional differences, with one copy dominant over the other, seem to be a relatively common feature of duplicated PCS genes across different plant families and originating from independent duplication events (e.g.…”

Differential paralog divergence modulates evolutionary outcomes in yeast

“…Many studies have aimed to determine whether adaptation and phenotypic change typically occur from mutations in non-coding or coding regions in the genome [44–48]. In the case of gene duplicates, it has been proposed that their retention provides genetic redundancy, buffering the mutational space to either acquire new function, or to partition the ancestral function between duplicates.…”