ArticleArchaea (Vancouver, B.C.)2014
A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life.
Article in Archaea (Vancouver, B.C.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment.Marine life science & technology · 2024Article
- The Compressed Vocabulary of Microbial Life.Frontiers in microbiology · 2021Article
- Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories.Scientific reports · 2020Article
- Bacterial Origin and Reductive Evolution of the CPR Group.Genome biology and evolution · 2020Article
- Descent of Bacteria and Eukarya From an Archaeal Root of Life.Evolutionary bioinformatics online · 2020Article
- More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases.Journal of molecular evolution · 2019Article
- Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.Evolutionary bioinformatics online · 2018Review
- The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data.PloS one · 2017Article
- Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life.Life (Basel, Switzerland) · 2016Article
- Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology.Computational and structural biotechnology journal · 2015Review
- A tree of cellular life inferred from a genomic census of molecular functions.Journal of molecular evolution · 2014Article
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3 authors.
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Abstract
The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent.
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