Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis , a wild relative of rice
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Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a “copy and paste” mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis , a wild relative of the Asian cultivated rice O. sativa , has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.
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The primary causes of TE depletion were reduction of LTR elements and DNA transposons, which are highly active element classes capable of rapid genome expansion.
“The primary causes of TE depletion were reduction of LTR elements and DNA transposons which are highly active element classes capable of rapid genome expansion (57–62).”
From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [59]
In “The genomic amplification of O. australiensis occurred after its speciation” (page unavailable), the paper says LTR-retrotransposons can be partially eliminated through recombination. It also describes LTR-retrotransposons as drivers of genome expansion. It does not identify reductions in both LTR elements and DNA transposons as the primary causes of the TE depletion claimed here. (LLM, conf=0.86)
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Sudasinghe, H., Matschiner, M., Britz, R., Conway, K. W., Tan, H. H., Salzburger, W., Peichel, C. L., & Rüber, L. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2614605123
- Authors
- Piegu, B., Guyot, R., Picault, N., Roulin, A., Saniyal, A., Kim, H., Collura, K., Brar, D. S., Jackson, S., Wing, R. A., & Panaud, O.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Purdue University West Lafayette (US)
- University of Arizona (US)
- International Rice Research Institute (PH)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2006-09-08
- Volume
- 16
- Issue
- 10
- Pages
- 1262-1269
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC1581435
- OpenAlex
- W7075735698
- Cited by
- 579
- References
- 1
- Citations by year
- 2026: 17 · 2025: 19 · 2024: 12 · 2023: 23 · 2022: 30 · 2021: 28 · 2020: 32 · 2019: 31 · 2018: 38 · 2017: 38 · 2016: 32 · 2015: 24 · 2014: 21 · 2013: 38 · 2012: 39
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Science Foundation (0208329, 0321678)
- Centre National de la Recherche Scientifique
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Taxonomy and Phylogenetics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Keywords
- retrotransposons, LTR retrotransposons, genome size evolution, Oryza australiensis, rice, wild rice, copy number expansion, transposable elements, polyploidy, rice wild relatives
- MeSH terms
- Base Sequence, Chromosome Mapping, Molecular Sequence Data, Phylogeny, Oryza, Blotting, Southern, Cluster Analysis, Sequence Analysis, DNA, Retroelements, Genome, Plant, Gene Duplication, Chromosomes, Artificial, Bacterial
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