Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion
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In analyzing gene families in the whole-genome sequences available for O. sativa (AA), O. glaberrima (AA), and O. brachyantha (FF), we observed large size expansions in the AA genomes compared to FF genomes for the super-families F-box and NB-ARC, and five additional families: the Aspartic proteases, BTB/POZ proteins (BTB), Glutaredoxins, Trypsin α-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.
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Rice has about 46,000 functioning genes that evolved over 15 million years.
“Rice (Oryza sativa), for example, has about 46,000 functioning genes that have evolved over 15 million years.2”
From The Gut Microbiome and the Brain (2014) · cites this paper as [2]
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The Gut Microbiome and the Brain
Galland, L. (2014) · Journal of Medicinal Food · doi:10.1089/jmf.2014.7000 · Cited by 648 · see citing works
- Authors
- Jacquemin, J., Ammiraju, J. S. S., Haberer, G., Billheimer, D. D., Yu, Y., Liu, L. C., Rivera, L. F., Mayer, K., Chen, M., & Wing, R. A.
- Affiliations
- University of Arizona (US)
- Helmholtz Munich (DE)
- Chinese Academy of Sciences (CN)
- ORCID
- Venue
- Molecular Plant
- Publisher
- Elsevier BV
- Published
- 2014-04
- Volume
- 7
- Issue
- 4
- Pages
- 642-656
- ISSN
- 1674-2052 (ISSN-L)
- OpenAlex
- W1992892352
- Cited by
- 54
- References
- 78
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 5 · 2023: 5 · 2022: 4 · 2021: 5 · 2020: 2 · 2019: 5 · 2018: 4 · 2017: 3 · 2016: 4 · 2015: 6 · 2014: 4
- FWCI
- 5.63
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Plant (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Site cant be reached (submittedVersion, other-oa)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Keywords
- Oryza, rice, gene family expansion, tandem duplication, gene loss, F-box genes, glutaredoxin, aspartic protease, purifying selection, positive selection, neofunctionalization, functional redundancy, Oryza glaberrima, Oryza brachyantha, genome evolution
- MeSH terms
- Biological Evolution, Oryza, Genome, Plant, Genes, Duplicate
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