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



Here, 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.



Loss 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.
Center for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark. hoffmann@plen.ku.dk.
Robert D
RD
Hoffmann
Center for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark.
Michael
M
Palmgren
D020413:3' Untranslated Regions; D017360:Arabidopsis / Q000235:genetics*; D001482:Base Composition; D001665:Binding Sites; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D007438:Introns; D016366:Open Reading Frames; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D022661:RNA, Untranslated; D012641:Selection, Genetic; D013312:Stress, Physiological; D020506:Untranslated Regions
D020413:3' Untranslated Regions; D022661:RNA, Untranslated; D020506:Untranslated Regions
3′ UTR; Arabidopsis thaliana; Conserved non-coding sequences; Evolution; Gene expression; Paralogous genes; Promoters; mRNA