ArticlePlant physiology2009
Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice.
Article in Plant physiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed, 143 citations in OpenAlex.
- A haplotype-resolved nutmeg genome reveals XY sex chromosome evolution and enables molecular sexing.Communications biology · 2026Article
- A Genome-Wide Pseudogene Map Reveals the Asymmetric Evolution of the A, B, and D Subgenomes in Common Wheat.Plants (Basel, Switzerland) · 2026Article
- Catalytic mechanism and transcriptional regulation of AtsTPS2 involved in germacrene A biosynthesis inFrontiers in plant science · 2026Article
- Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao.G3 (Bethesda, Md.) · 2025Article
- Identification and structural characterization of pseudogenes in Fusarium graminearum.Scientific reports · 2025Article
- The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms.Nature communications · 2025Article
- Development of a 101.6K liquid-phased probe for GWAS and genomic selection in pine wilt disease-resistance breeding in Masson pine.The plant genome · 2025Article
- Transcriptome analysis of the allotetraploids of the Dilatata group of Paspalum (Poaceae): effects of diploidization on the expression of defensin and Snakin/GASA genes.Functional & integrative genomics · 2024Article
- Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.Nature genetics · 2024Article
- Overexpression of theFrontiers in plant science · 2024Article
- The Snapdragon Genomes Reveal the Evolutionary Dynamics of the S-Locus Supergene.Molecular biology and evolution · 2023Article
- Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies.Plant communications · 2023Article
- Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions.Journal of advanced research · 2022Article
- Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement.Journal of advanced research · 2022Article
- Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding.Nature communications · 2022Article
- Ovule siRNAs methylate protein-coding genes in trans.The Plant cell · 2022Article
- Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates.Plant biotechnology journal · 2022Article
- In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue.PLoS genetics · 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
- Structural characterization and duplication modes of pseudogenes in plants.Scientific reports · 2021Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudogenes (Psi) are nonfunctional genomic sequences resembling functional genes. Knowledge of Psis can improve genome annotation and our understanding of genome evolution. However, there has been relatively little systemic study of Psis in plants. In this study, we characterized the evolution and expression patterns of Psis in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). In contrast to animal Psis, many plant Psis experienced much stronger purifying selection. In addition, plant Psis experiencing stronger selective constraints tend to be derived from relatively ancient duplicates, suggesting that they were functional for a relatively long time but became Psis recently. Interestingly, the regions 5' to the first stops in the Psis have experienced stronger selective constraints compared with 3' regions, suggesting that the 5' regions were functional for a longer period of time after the premature stops appeared. We found that few Psis have expression evidence, and their expression levels tend to be lower compared with annotated genes. Furthermore, Psis with expressed sequence tags tend to be derived from relatively recent duplication events, indicating that Psi expression may be due to insufficient time for complete degeneration of regulatory signals. Finally, larger protein domain families have significantly more Psis in general. However, while families involved in environmental stress responses have a significant excess of Psis, transcription factors and receptor-like kinases have lower than expected numbers of Psis, consistent with their elevated retention rate in plant genomes. Our findings illustrate peculiar properties of plant Psis, providing additional insight into the evolution of duplicate genes and benefiting future genome annotation.
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