ArticleGenome biology2011
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed.
- Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model.Journal of molecular evolution · 2025Article
- NGATHA carpel development genes evolved in the common ancestor of seed plants.The Plant journal : for cell and molecular biology · 2025Article
- Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.Genome biology and evolution · 2024Article
- Article
- Gene loss during a transition to multicellularity.Scientific reports · 2023Article
- The role of mitochondrial energetics in the origin and diversification of eukaryotes.Nature ecology & evolution · 2022Article
- Massive Loss of Transcription Factors Promotes the Initial Diversification of Placental Mammals.International journal of molecular sciences · 2022Article
- Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.Cell genomics · 2022Article
- Genomic evolution of the Coronaviridae family.Virology · 2022Article
- GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.BMC genomics · 2021Article
- Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes.Briefings in bioinformatics · 2021Article
- Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity.Genome biology and evolution · 2021Article
- The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition.Open biology · 2021Review
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
- The modular nature of protein evolution: domain rearrangement rates across eukaryotic life.BMC evolutionary biology · 2020Article
- Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences.PLoS computational biology · 2019Article
- Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).Virology · 2019Article
- Patterns of Conservation and Diversification in the Fungal Polarization Network.Genome biology and evolution · 2018Article
- Improving pairwise comparison of protein sequences with domain co-occurrence.PLoS computational biology · 2018Article
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2 authors.
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Abstract
backgroundGenome size and complexity, as measured by the number of genes or protein domains, is remarkably similar in most extant eukaryotes and generally exhibits no correlation with their morphological complexity. Underlying trends in the evolution of the functional content and capabilities of different eukaryotic genomes might be hidden by simultaneous gains and losses of genes.
resultsWe reconstructed the domain repertoires of putative ancestral species at major divergence points, including the last eukaryotic common ancestor (LECA). We show that, surprisingly, during eukaryotic evolution domain losses in general outnumber domain gains. Only at the base of the animal and the vertebrate sub-trees do domain gains outnumber domain losses. The observed gain/loss balance has a distinct functional bias, most strikingly seen during animal evolution, where most of the gains represent domains involved in regulation and most of the losses represent domains with metabolic functions. This trend is so consistent that clustering of genomes according to their functional profiles results in an organization similar to the tree of life. Furthermore, our results indicate that metabolic functions lost during animal evolution are likely being replaced by the metabolic capabilities of symbiotic organisms such as gut microbes.
conclusionsWhile protein domain gains and losses are common throughout eukaryote evolution, losses oftentimes outweigh gains and lead to significant differences in functional profiles. Results presented here provide additional arguments for a complex last eukaryotic common ancestor, but also show a general trend of losses in metabolic capabilities and gain in regulatory complexity during the rise of animals.
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