ArticlePloS one2016
Evolution of the Exon-Intron Structure in Ciliate Genomes.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The shortest animal introns: insights from parasitic cnidarians.Molecular biology and evolution · 2026Article
- Genomic survey and expression analysis of the CDPK genes in Liriodendron Chinense to explore their potential functions under multiple abiotic stresses.BMC genomics · 2026Article
- Entropy-driven machine learning for deciphering mRNA rearrangement by splicing in complex microorganisms.Frontiers in bioinformatics · 2026Article
- Whole-genome duplications revealed by macronuclear genomes of five rare species of the model ciliates Paramecium.Science China. Life sciences · 2025Article
- Genome-wide identification and expression analysis of ACS and ACO gene family in Ziziphus jujuba mill during fruit ripening.Scientific reports · 2025Article
- Nuclear dualism without extensive DNA elimination in the ciliateProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics inInternational journal of molecular sciences · 2024Article
- Genome-wide analysis of plant specific YABBY transcription factor gene family in carrot (Dacus carota) and its comparison with Arabidopsis.BMC genomic data · 2024Article
- Genome-wide in-silico analysis of ethylene biosynthesis gene family in Musa acuminata L. and their response under nutrient stress.Scientific reports · 2024Article
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- Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses.Scientific reports · 2023Article
- Genome-Wide Identification and Characterization of the Biosynthesis of the Polyamine Gene Family inGenes · 2023Article
- Nontriplet feature of genetic code inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genome-wide identification, classification, and characterization of lectin gene superfamily in sweet orange (Citrus sinensis L.).PloS one · 2023Article
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- Intronization Signatures in Coding Exons Reveal the Evolutionary Fluidity of Eukaryotic Gene Architecture.Microorganisms · 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
- Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis,Royal Society open science · 2021Article
- Identification and Expression Analysis of Sugar Transporter Gene Family inInternational journal of genomics · 2020Article
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2 authors.
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Abstract
A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n) are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively), but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33-35 bp, 47-51 bp, and 78-80 bp). In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short introns in various representatives of Ciliates.
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