ArticleProceedings of the National Academy of Sciences of the United States of America2002
Large-scale comparison of intron positions among animal, plant, and fungal genes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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97 citing papers in PubMed, 191 citations in OpenAlex.
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- Intron turnover of slc26a1 and slc26a2 and convergence of intron insertion sites.Scientific reports · 2025Article
- Discovering Intron Gain Events in Humans Through Large-Scale Evolutionary Comparisons.Genome biology and evolution · 2025Article
- De Novo Creation of Two Novel Spliceosomal Introns of RECG1 by Intronization of Formerly Exonic Sequences in Orchidaceae.Journal of molecular evolution · 2025Article
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- Analysis of non-coding small RNA similarity/sharing between plant and animal genomes.Science China. Life sciences · 2023Article
- New Insights into the Evolution and Gene Structure of the Mitochondrial Carrier Family Unveiled by Analyzing the Frequent and Conserved Intron Positions.Molecular biology and evolution · 2023Article
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- MYB transcription factor family in sweet cherry (Prunus avium L.): genome-wide investigation, evolution, structure, characterization and expression patterns.BMC plant biology · 2022Article
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- Genome-wide identification and expression analysis of NtbHLH gene family in tobacco (Plant diversity · 2021Article
- Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat (Frontiers in genetics · 2021Article
- Comprehensive database and evolutionary dynamics of U12-type introns.Nucleic acids research · 2020Article
- Editorial: Alternative Splicing Regulation in Plants.Frontiers in plant science · 2020Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We purge large databases of animal, plant, and fungal intron-containing genes to a 20% similarity level and then identify the most similar animal-plant, animal-fungal, and plant-fungal protein pairs. We identify the introns in each BLAST 2.0 alignment and score matched intron positions and slid (near-matched, within six nucleotides) intron positions automatically. Overall we find that 10% of the animal introns match plant positions, and a further 7% are "slides." Fifteen percent of fungal introns match animal positions, and 13% match plant positions. Furthermore, the number of alignments with high numbers of matches deviates greatly from the Poisson expectation. The 30 animal-plant alignments with the highest matches (for which 44% of animal introns match plant positions) when aligned with fungal genes are also highly enriched for triple matches: 39% of the fungal introns match both animal and plant positions. This is strong evidence for ancestral introns predating the animal-plant-fungal divergence, and in complete opposition to any expectations based on random insertion. In examining the slid introns, we show that at least half are caused by imperfections in the alignments, and are most likely to be actual matches at common positions. Thus, our final estimates are that approximately equal 14% of animal introns match plant positions, and that approximately equal 17-18% of fungal introns match animal or plant positions, all of these being likely to be ancestral in the eukaryotes.
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