ArticleThe Plant cell2014
Pollen-specific activation of Arabidopsis retrogenes is associated with global transcriptional reprogramming.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 25 citations in OpenAlex.
- Novel insights into retrogene evolution and cold adaptation in the alpine plant Crucihimalaya himalaica (Brassicaceae).BMC biology · 2026Article
- Sophora genomes provide insight into the evolution of alkaloid metabolites along with small-scale gene duplication.BMC genomics · 2023Article
- Structural characterization and duplication modes of pseudogenes in plants.Scientific reports · 2021Article
- Rapid Genome Evolution and Adaptation ofFrontiers in plant science · 2021Article
- Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations.Computational and structural biotechnology journal · 2021Article
- RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization.Frontiers in genetics · 2021Article
- The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development.The Plant cell · 2019Article
- Rapid functional divergence after small-scale gene duplication in grasses.BMC evolutionary biology · 2019Article
- Expansion ofHorticulture research · 2019Article
- The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?Genome biology and evolution · 2017Article
- Protein-Coding Genes' Retrocopies and Their Functions.Viruses · 2017Review
- Functional characterization of open chromatin in bidirectional promoters of rice.Scientific reports · 2016Article
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots.Scientific reports · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Duplications allow for gene functional diversification and accelerate genome evolution. Occasionally, the transposon amplification machinery reverse transcribes the mRNA of a gene, integrates it into the genome, and forms an RNA-duplicated copy: the retrogene. Although retrogenes have been found in plants, their biology and evolution are poorly understood. Here, we identified 251 (216 novel) retrogenes in Arabidopsis thaliana, corresponding to 1% of protein-coding genes. Arabidopsis retrogenes are derived from ubiquitously transcribed parents and reside in gene-rich chromosomal regions. Approximately 25% of retrogenes are cotranscribed with their parents and 3% with head-to-head oriented neighbors. This suggests transcription by novel promoters for 72% of Arabidopsis retrogenes. Many retrogenes reach their transcription maximum in pollen, the tissue analogous to animal spermatocytes, where upregulation of retrogenes has been found previously. This implies an evolutionarily conserved mechanism leading to this transcription pattern of RNA-duplicated genes. During transcriptional repression, retrogenes are depleted of permissive chromatin marks without an obvious enrichment for repressive modifications. However, this pattern is common to many other pollen-transcribed genes independent of their evolutionary origin. Hence, retroposition plays a role in plant genome evolution, and the developmental transcription pattern of retrogenes suggests an analogous regulation of RNA-duplicated genes in plants and animals.
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