ArticlePLoS genetics2014
Recurrent loss of specific introns during angiosperm evolution.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Chloroplast genome sequencing of Poa pratensis and comparative chloroplast genomics analysis with other 29 grass species.Functional & integrative genomics · 2026Article
- Comprehensive analysis of the sucrose nonfermenting 1-related protein kinase 2 gene family in broomcorn millet (Panicum miliaceum L.) under abiotic stress conditions.BMC genomics · 2025Article
- Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote.BMC biology · 2024Article
- 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
- Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses.Scientific reports · 2023Article
- Intron losses and gains in the nematodes.Biology direct · 2022Article
- Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane.Journal of experimental botany · 2022Article
- Characterization and evolutionary diversification of the phospholipase D gene family in mosses.Frontiers in genetics · 2022Article
- An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence.Evolutionary bioinformatics online · 2021Article
- Article
- The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy.Genes & genomics · 2020Review
- Novel B-chromosome-specific transcriptionally active sequences are present throughout the maize B chromosome.Molecular genetics and genomics : MGG · 2020Article
- Genome-wide analysis and evolution of plant thaumatin-like proteins: a focus on the origin and diversification of osmotins.Molecular genetics and genomics : MGG · 2019Article
- Article
- Parallel loss of introns in the ABCB1 gene in angiosperms.BMC evolutionary biology · 2017Article
- Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs).Genome biology and evolution · 2017Article
- Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium.BMC evolutionary biology · 2015Article
- Evolutionary Character of Alternative Splicing in Plants.Bioinformatics and biology insights · 2015Review
- Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns.PloS one · 2015Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous instances of presence/absence variations for introns have been documented in eukaryotes, and some cases of recurrent loss of the same intron have been suggested. However, there has been no comprehensive or phylogenetically deep analysis of recurrent intron loss. Of 883 cases of intron presence/absence variation that we detected in five sequenced grass genomes, 93 were confirmed as recurrent losses and the rest could be explained by single losses (652) or single gains (118). No case of recurrent intron gain was observed. Deep phylogenetic analysis often indicated that apparent intron gains were actually numerous independent losses of the same intron. Recurrent loss exhibited extreme non-randomness, in that some introns were removed independently in many lineages. The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium. Adjacent introns and small introns were found to be preferentially lost. Intron loss genes exhibited a high frequency of germ line or early embryogenesis expression. In addition, flanking exon A+T-richness and intron TG/CG ratios were higher in retained introns. This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss. This study provides the first comprehensive analysis of recurrent intron loss, makes a series of novel findings on the patterns of recurrent intron loss during the evolution of the grass family, and provides insight into the molecular mechanism(s) underlying intron loss.
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