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Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications.
Mol Biol Evol. 2012 Nov; 29(11):3541-51.MB

Abstract

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.

Authors+Show Affiliations

Instituto de Biologia Molecular y Celular de Plantas-IBMCP (CSIC-UPV), Integrative Systems Biology Group, Valencia, Spain.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

22734049

Citation

Carretero-Paulet, Lorenzo, and Mario A. Fares. "Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed By Whole and Small-scale Genome Duplications." Molecular Biology and Evolution, vol. 29, no. 11, 2012, pp. 3541-51.
Carretero-Paulet L, Fares MA. Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. Mol Biol Evol. 2012;29(11):3541-51.
Carretero-Paulet, L., & Fares, M. A. (2012). Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. Molecular Biology and Evolution, 29(11), 3541-51. https://doi.org/10.1093/molbev/mss162
Carretero-Paulet L, Fares MA. Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed By Whole and Small-scale Genome Duplications. Mol Biol Evol. 2012;29(11):3541-51. PubMed PMID: 22734049.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. AU - Carretero-Paulet,Lorenzo, AU - Fares,Mario A, Y1 - 2012/06/24/ PY - 2012/6/27/entrez PY - 2012/6/27/pubmed PY - 2013/3/6/medline SP - 3541 EP - 51 JF - Molecular biology and evolution JO - Mol. Biol. Evol. VL - 29 IS - 11 N2 - 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. SN - 1537-1719 UR - https://www.unboundmedicine.com/medline/citation/22734049/Evolutionary_dynamics_and_functional_specialization_of_plant_paralogs_formed_by_whole_and_small_scale_genome_duplications_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/mss162 DB - PRIME DP - Unbound Medicine ER -