ArticleThe Plant cell2019
Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants.
Article in The Plant cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 45 citations in OpenAlex.
- Clusia genomes shed light on the evolution and diversity of crassulacean acid metabolism physiotypes.Nature communications · 2026Article
- High-quality genome assembly of Aglaia odorata reveals evolution, terpenes diversity and abundance in Meliaceae.Molecular horticulture · 2026Article
- Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene.Genome biology · 2026Article
- 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
- Transposon-Associated Small RNAs Involved in Plant Defense in Poplar.Plants (Basel, Switzerland) · 2025Article
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- From the archives: evolutionary origins of Delphinieae flowers, pseudogenes, and the light-responsive localization of COP1.The Plant cell · 2024Article
- Balanophora genomes display massively convergent evolution with other extreme holoparasites and provide novel insights into parasite-host interactions.Nature plants · 2023Article
- Enhanced genome-wide association reveals the role of YABBY11-NGATHA-LIKE1 in leaf serration development of Populus.Plant physiology · 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
- Miniature Inverted-repeat Transposable Elements Drive Rapid MicroRNA Diversification in Angiosperms.Molecular biology and evolution · 2022Article
- Diversity and Functional Evolution of Terpene Synthases in Rosaceae.Plants (Basel, Switzerland) · 2022Article
- Evolutionary research on the expansin protein family during the plant transition to land provides new insights into the development of Tartary buckwheat fruit.BMC genomics · 2021Article
- Structural characterization and duplication modes of pseudogenes in plants.Scientific reports · 2021Article
- Genome-Wide Analysis of Coding and Non-coding RNA Reveals a Conserved miR164-NAC-mRNA Regulatory Pathway for Disease Defense inFrontiers in genetics · 2021Article
- Computational Methods for Pseudogene Annotation Based on Sequence Homology.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Roles of Non-Coding RNAs in Response to Nitrogen Availability in Plants.International journal of molecular sciences · 2020Review
- Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation.Plant communications · 2020Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudogenes (Ψs), nonfunctional relatives of functional genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Evolutionary analysis provides clues to Ψ origins and effects on gene regulation. However, few systematic studies of plant Ψs have been conducted, hampering comparative analyses. Here, we examined the origin, evolution, and expression patterns of Ψs and their relationships with noncoding sequences in seven angiosperm plants. We identified ∼250,000 Ψs, most of which are more lineage specific than protein-coding genes. The distribution of Ψs on the chromosome indicates that genome recombination may contribute to Ψ elimination. Most Ψs evolve rapidly in terms of sequence and expression levels, showing tissue- or stage-specific expression patterns. We found that a surprisingly large fraction of nontransposable element regulatory noncoding RNAs (microRNAs and long noncoding RNAs) originate from transcription of Ψ proximal upstream regions. We also found that transcription factor binding sites preferentially occur in putative Ψ proximal upstream regions compared with random intergenic regions, suggesting that Ψs have conditioned genome evolution by providing transcription factor binding sites that serve as promoters and enhancers. We therefore propose that rapid rewiring of Ψ transcriptional regulatory regions is a major mechanism driving the origin of novel regulatory modules.
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