ArticleThe Plant cell2009
The functional role of pack-MULEs in rice inferred from purifying selection and expression profile.
Article in The Plant cell, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Review
- The genetic heist: how transposable elements capture and repurpose genes in plants.Genome biology · 2026Review
- Ubiquitin-like SUMO protease expansion in rice (Oryza sativa L.).The plant genome · 2026Article
- Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.Nature communications · 2026Article
- The role of mobile DNA elements in the dynamics of plant genome plasticity.Journal of experimental botany · 2025Review
- Functional innovation through new genes as a general evolutionary process.Nature genetics · 2025Review
- Exploring the complexity of genome size reduction in angiosperms.Plant molecular biology · 2024Review
- Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.Horticulture research · 2024Article
- Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to PlantPlants (Basel, Switzerland) · 2023Review
- Micro and macroevolution of sea anemone venom phenotype.Nature communications · 2023Article
- Miniature Inverted-repeat Transposable Elements Drive Rapid MicroRNA Diversification in Angiosperms.Molecular biology and evolution · 2022Article
- An Eruption of LTR Retrotransposons in the Autopolyploid Genomes ofPlants (Basel, Switzerland) · 2022Article
- Repeatome-Based Phylogenetics in Pelargonium Section Ciconium (Sweet) Harvey.Genome biology and evolution · 2021Article
- Review
- DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans.Nature communications · 2021Article
- Reprogramming of Retrotransposon Activity during Speciation of the Genus Citrus.Genome biology and evolution · 2019Article
- GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals.Genome biology and evolution · 2019Article
- Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling.Nucleic acids research · 2019Article
- Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene.Mobile DNA · 2019Article
- Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes.BMC genomics · 2018Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.
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