ArticleProceedings of the National Academy of Sciences of the United States of America2014
Comparative analysis of pseudogenes across three phyla.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 107 citations in OpenAlex.
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- Methylation array signals are predictive of chronological age without bisulfite conversion.GeroScience · 2026Article
- A Genome-Wide Pseudogene Map Reveals the Asymmetric Evolution of the A, B, and D Subgenomes in Common Wheat.Plants (Basel, Switzerland) · 2026Article
- Retention of a singlebioRxiv : the preprint server for biology · 2025Article
- Systematic analysis of noncanonical ribosomal protein paralogs does not provide evidence for specialized functions inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Transcript Patterns of BovineGenes · 2025Article
- Gene-Pseudogene Inversions as a Hidden Source of Missing Heritability.medRxiv : the preprint server for health sciences · 2025Article
- Identification and structural characterization of pseudogenes in Fusarium graminearum.Scientific reports · 2025Article
- Pseudogenes in the carcinogenesis: epithelial-to-mesenchymal transition process and cancer initiating cells.Reports of practical oncology and radiotherapy : journal of Greatpoland Cancer Center in Poznan and Polish Society of Radiation Oncology · 2025Review
- The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of "retrobiome" in naked mole rat.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The annotation ofScience advances · 2024Article
- The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles.Evolutionary bioinformatics online · 2024Article
- Human-specific features and developmental dynamics of the brain N-glycome.Science advances · 2023Article
- Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies.Molecular biology and evolution · 2023Article
- Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities.Genomics, proteomics & bioinformatics · 2023Article
- Evolution and function of developmentally dynamic pseudogenes in mammals.Genome biology · 2022Article
- Structural and developmental dynamics of Matrix associated regions in Drosophila melanogaster genome.BMC genomics · 2022Article
- Extensive nrDNA ITS polymorphism inFrontiers in plant science · 2022Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors at 3 institutions in 2 countries.
Funding
Abstract
Pseudogenes are degraded fossil copies of genes. Here, we report a comparison of pseudogenes spanning three phyla, leveraging the completed annotations of the human, worm, and fly genomes, which we make available as an online resource. We find that pseudogenes are lineage specific, much more so than protein-coding genes, reflecting the different remodeling processes marking each organism's genome evolution. The majority of human pseudogenes are processed, resulting from a retrotranspositional burst at the dawn of the primate lineage. This burst can be seen in the largely uniform distribution of pseudogenes across the genome, their preservation in areas with low recombination rates, and their preponderance in highly expressed gene families. In contrast, worm and fly pseudogenes tell a story of numerous duplication events. In worm, these duplications have been preserved through selective sweeps, so we see a large number of pseudogenes associated with highly duplicated families such as chemoreceptors. However, in fly, the large effective population size and high deletion rate resulted in a depletion of the pseudogene complement. Despite large variations between these species, we also find notable similarities. Overall, we identify a broad spectrum of biochemical activity for pseudogenes, with the majority in each organism exhibiting varying degrees of partial activity. In particular, we identify a consistent amount of transcription (∼15%) across all species, suggesting a uniform degradation process. Also, we see a uniform decay of pseudogene promoter activity relative to their coding counterparts and identify a number of pseudogenes with conserved upstream sequences and activity, hinting at potential regulatory roles.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.