ArticleJournal of molecular evolution2006
Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome.
Article in Journal of molecular evolution, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 41 citations in OpenAlex.
- Nuku, a family of primate retrocopies derived from KU70.G3 (Bethesda, Md.) · 2021Article
- Structural characterization and duplication modes of pseudogenes in plants.Scientific reports · 2021Article
- Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition.3 Biotech · 2021Article
- A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.PloS one · 2019Article
- Protein-Coding Genes' Retrocopies and Their Functions.Viruses · 2017Review
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- Gene-pseudogene evolution: a probabilistic approach.BMC genomics · 2015Article
- RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity.International journal of evolutionary biology · 2013Article
- Parallel relaxation of stringent RNA recognition in plant and mammalian L1 retrotransposons.Molecular biology and evolution · 2012Article
- Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions.PloS one · 2012Article
- Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2011Article
- Pseudogenes: pseudo-functional or key regulators in health and disease?RNA (New York, N.Y.) · 2011Review
- Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function.BMC evolutionary biology · 2011Article
- Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris.The Plant cell · 2010Article
- Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice.Plant physiology · 2009Article
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Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We identified 411 processed sequences in the Arabidopsis thaliana genome based on the fact that they have lost their intron(s) and have a length that is at least 95% of the length of the gene that gave rise to them. These sequences were generated by 230 different genes and clearly originated from retrotranspositons events because most of them (91%) have a poly(A)-tail. They are composed of 376 sequences with frame shifts and/or premature stop codons (processed pseudogenes) and 35 sequences without disablements (processed genes). Eleven of these processed genes are likely functional retrotransposed genes because they have low Ka/Ks ratios and high Ks values, and their sequences match numerous Arabidopsis ESTs. Processed sequences are mostly randomly distributed in the Arabidopsis genome and their rate of accumulation has steadily been decreasing since it peaked some 50 MYA. In contrast with the situation observed in mammals, the processed sequences found in the Arabidopsis genome originate from genes with high copy numbers and not from highly expressed genes. The patterns of spontaneous mutations in Arabidopsis are slightly different than those of mammals but are similar to those observed in Drosophila. This suggests that methylated cytosine deamination is less frequent in Arabidopsis than in mammals.
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