ArticlePloS one2012
Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- A Genome-Wide Pseudogene Map Reveals the Asymmetric Evolution of the A, B, and D Subgenomes in Common Wheat.Plants (Basel, Switzerland) · 2026Article
- Evolutionary patterns of nucleotide substitution rates in plastid genomes ofEcology and evolution · 2021Article
- Mapping QTLs for 15 morpho-metric traits inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Large-scale identification and functional analysis ofProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana.Molecular biology and evolution · 2019Article
- A gene graveyard in the genome of the fungus Podospora comata.Molecular genetics and genomics : MGG · 2019Article
- Comprehensive analysis of NAC transcription factors and their expression during fruit spine development in cucumber (Horticulture research · 2018Article
- High genetic abundance of Rpi-blb2/Mi-1.2/Cami gene family in Solanaceae.BMC evolutionary biology · 2015Article
- Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana.Plant physiology · 2015Article
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Corrections and comments
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ψs utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ψs within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ∼28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ψs on chromosomes showed a significantly negative correlation between Ψs/ORFs and their local gene densities, suggesting a higher proportion of Ψs in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Ψ loci, even the intact coding sequences (CDSs) in the Ψ loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ψs mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.
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