Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications

Abstract

[EN] Gene duplicates are a major source of evolutionary novelties in the form of new or specialized functions and play a key role in speciation. Gene duplicates are generated through whole genome duplications (WGD) or small-scale genome duplications (SSD). Although WGD preserves the stoichiometric relationships between duplicates, those arising from SSD are usually unbalanced and are expected to follow different evolutionary dynamics than those formed by WGD. To dissect the role of the mechanism of duplication in these differential dynamics and determine whether this role was shared across species, we performed a genome wide evolutionary analysis of gene duplications arising from the most recent WGD events and contemporary episodes of SSD in four model species representing distinct plant evolutionary lineages. We found an excess of relaxed purifying selection after duplication in SSD paralogs compared with WGD, most of which may have been the result of functional divergence events between gene copies as estimated by measures of genetic distances. These differences were significant in three angiosperm genomes but not in the moss species Physcomitrella patens. Although the comparison of models of evolution does not attribute a relevant role to the mechanism of duplication in the evolution duplicates, distribution of retained genes among Gene Ontology functional categories support the conclusion that evolution of gene duplicates depends on its origin of duplication (WGD and SSD) but, most importantly, on the species. Similar lineage-specific biases were also observed in protein network connectivity, translational efficiency, and selective constraints acting on synonymous codon usage. Although the mechanism of duplication may determine gene retention, our results attribute a dominant role to the species in determining the ultimate pattern of duplicate gene retention and reveal an unanticipated complexity in the evolutionary dynamics and functional specialization of duplicated genes in plants.This work has been performed making extensive use of PERL scripts and Bioperl and R packages. The authors thank the Bioperl community for continuous support. They are especially grateful to Ken Wolfe, Santiago F Elena, David L Robertson, and Manuel Rodriguez-Concepcion for critical reading of the manuscript. This work was supported by a grant from the Spanish Ministerio de Ciencia e Inovacion (BFU2009-12022) and a grant of the Research Frontiers Program (10/RFP/GEN2685) from Science Foundation Ireland.Carretero Paulet, L.; Fares Riaño, MA. (2012). Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. 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