ArticlePlant physiology2014
Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.
Article in Plant physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Kingdom-wide evolutionary characterization of RNA editing factors in Archaeplastida.Molecular biology and evolution · 2026Article
- Novel insights into retrogene evolution and cold adaptation in the alpine plant Crucihimalaya himalaica (Brassicaceae).BMC biology · 2026Article
- Identification and structural characterization of pseudogenes in Fusarium graminearum.Scientific reports · 2025Article
- Gene fusion as an important mechanism to generate new genes in the genus Oryza.Genome biology · 2022Article
- Genome-wide identification and expression analysis of bZIP transcription factors in oil palm (Elaeis guineensis Jacq.) under abiotic stress.Protoplasma · 2022Article
- Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability.Rice (New York, N.Y.) · 2021Article
- Draft genome sequence of the Antarctic green algaiScience · 2021Article
- Rapid Genome Evolution and Adaptation ofFrontiers in plant science · 2021Article
- Improved ontology for eukaryotic single-exon coding sequences in biological databases.Database : the journal of biological databases and curation · 2018Article
- New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication.Genome biology · 2017Article
- Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events.Molecular biology and evolution · 2017Article
- The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?Genome biology and evolution · 2017Article
- Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in Drosophila.BMC cell biology · 2017Article
- LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots.Scientific reports · 2016Article
- Functional Divergence of Diterpene Syntheses in the Medicinal Plant Salvia miltiorrhiza.Plant physiology · 2015Article
- Evolutionary Character of Alternative Splicing in Plants.Bioinformatics and biology insights · 2015Review
Corrections and comments
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4 authors.
Funding
Abstract
The structure of eukaryotic genes evolves extensively by intron loss or gain. Previous studies have revealed two models for gene structure evolution through the loss of introns: RNA-based gene conversion, dubbed the Fink model and retroposition model. However, retrogenes that experienced both intron loss and intron-retaining events have been ignored; evolutionary processes responsible for the variation in complex exon-intron structure were unknown. We detected hundreds of retroduplication-derived genes in human (Homo sapiens), fly (Drosophila melanogaster), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) and categorized them either as duplicated genes that have all introns lost or as duplicated genes that have at least lost one and retained one intron compared with the parental copy (intron-retaining [IR] type). Our new model attributes intron retention alternative splicing to the generation of these IR-type gene pairs. We presented 25 parental genes that have an intron retention isoform and have retained introns in the same locations in the IR-type duplicate genes, which directly support our hypothesis. Our alternative-splicing-based model in conjunction with the retroposition and Fink models can explain the IR-type gene observed. We discovered a greater percentage of IR-type genes in plants than in animals, which may be due to the abundance of intron retention cases in plants. Given the prevalence of intron retention in plants, this new model gives a support that plant genomes have very complex gene structures.
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