ArticlePLoS computational biology2012
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Evolution of protein domains and protein domain combinations provides insights into the origin and diversification of land plants.Cell genomics · 2026Article
- Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model.Journal of molecular evolution · 2025Article
- The highly dynamic pangenome of basal chordates is enriched in defence and immunity genes and is inherited following the Mendelian law.PLoS genetics · 2025Article
- Tracing the paths of modular evolution by quantifying rearrangement events of protein domains.BMC ecology and evolution · 2025Article
- Genomic evolution of the Coronaviridae family.Virology · 2022Article
- Article
- Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human PathogenicMicroorganisms · 2021Article
- Protein Surface Interactions-Theoretical and Experimental Studies.Frontiers in molecular biosciences · 2021Review
- Review
- Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).Virology · 2019Article
- Article
- Similar Ratios of Introns to Intergenic Sequence across Animal Genomes.Genome biology and evolution · 2017Article
- Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.Genomics, proteomics & bioinformatics · 2016Article
- Evolution of Protein Domain Repeats in Metazoa.Molecular biology and evolution · 2016Article
- The language of the protein universe.Current opinion in genetics & development · 2015Review
- AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.Bioinformatics (Oxford, England) · 2015Article
- The robustness of a signaling complex to domain rearrangements facilitates network evolution.PLoS biology · 2014Article
- New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM.Genome biology and evolution · 2014Article
- AIDA: ab initio domain assembly server.Nucleic acids research · 2014Article
- Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.PLoS computational biology · 2014Article
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2 authors.
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Abstract
Evolutionary innovation in eukaryotes and especially animals is at least partially driven by genome rearrangements and the resulting emergence of proteins with new domain combinations, and thus potentially novel functionality. Given the random nature of such rearrangements, one could expect that proteins with particularly useful multidomain combinations may have been rediscovered multiple times by parallel evolution. However, existing reports suggest a minimal role of this phenomenon in the overall evolution of eukaryotic proteomes. We assembled a collection of 172 complete eukaryotic genomes that is not only the largest, but also the most phylogenetically complete set of genomes analyzed so far. By employing a maximum parsimony approach to compare repertoires of Pfam domains and their combinations, we show that independent evolution of domain combinations is significantly more prevalent than previously thought. Our results indicate that about 25% of all currently observed domain combinations have evolved multiple times. Interestingly, this percentage is even higher for sets of domain combinations in individual species, with, for instance, 70% of the domain combinations found in the human genome having evolved independently at least once in other species. We also show that previous, much lower estimates of this rate are most likely due to the small number and biased phylogenetic distribution of the genomes analyzed. The process of independent emergence of identical domain combination is widespread, not limited to domains with specific functional categories. Besides data from large-scale analyses, we also present individual examples of independent domain combination evolution. The surprisingly large contribution of parallel evolution to the development of the domain combination repertoire in extant genomes has profound consequences for our understanding of the evolution of pathways and cellular processes in eukaryotes and for comparative functional genomics.
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