ArticlePLoS computational biology2011
A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
- Identity rather than 3D position informs splicing of rare introns in the human genome.iScience · 2026Article
- Horizontal transmission of functionally diverse transposons is a major source of new introns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deletion of splicing factor Cdc5 in Toxoplasma disrupts transcriptome integrity, induces abortive bradyzoite formation, and prevents acute infection in mice.Nature communications · 2025Article
- Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron-Exon Gene Structures Across Eukaryotic Lineages.Molecular biology and evolution · 2024Article
- Taxonomy of introns and the evolution of minor introns.Nucleic acids research · 2024Article
- Transposon-derived introns as an element shaping the structure of eukaryotic genomes.Mobile DNA · 2024Review
- Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.Genome biology and evolution · 2024Article
- C and G are frequently mutated into T and A in coding regions of human genes.Molecular genetics and genomics : MGG · 2024Article
- Comparative Genome Annotation.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Article
- Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome.Molecular biology and evolution · 2023Article
- Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor.Molecular biology and evolution · 2023Article
- Introns: the "dark matter" of the eukaryotic genome.Frontiers in genetics · 2023Review
- Trends in the evolution of intronless genes inFrontiers in plant science · 2023Article
- A broadly conserved fungal alcohol oxidase (AOX) facilitates fungal invasion of plants.Molecular plant pathology · 2023Article
- Transposable elements drive intron gain in diverse eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Intronization Signatures in Coding Exons Reveal the Evolutionary Fluidity of Eukaryotic Gene Architecture.Microorganisms · 2022Article
- Intron losses and gains in the nematodes.Biology direct · 2022Article
- The spread of the first introns in proto-eukaryotic paralogs.Communications biology · 2022Article
- Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation?Integrative organismal biology (Oxford, England) · 2022Article
44 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages. Vertebrates, some invertebrates and green plants have intron-rich genes, with 6-7 introns per kilobase of coding sequence, whereas most of the other eukaryotes have intron-poor genes. We reconstructed the history of intron gain and loss using a probabilistic Markov model (Markov Chain Monte Carlo, MCMC) on 245 orthologous genes from 99 genomes representing the three of the five supergroups of eukaryotes for which multiple genome sequences are available. Intron-rich ancestors are confidently reconstructed for each major group, with 53 to 74% of the human intron density inferred with 95% confidence for the Last Eukaryotic Common Ancestor (LECA). The results of the MCMC reconstruction are compared with the reconstructions obtained using Maximum Likelihood (ML) and Dollo parsimony methods. An excellent agreement between the MCMC and ML inferences is demonstrated whereas Dollo parsimony introduces a noticeable bias in the estimations, typically yielding lower ancestral intron densities than MCMC and ML. Evolution of eukaryotic genes was dominated by intron loss, with substantial gain only at the bases of several major branches including plants and animals. The highest intron density, 120 to 130% of the human value, is inferred for the last common ancestor of animals. The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing.
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