Processed Pseudogenes, Processed Genes, and Spontaneous Mutations in the Arabidopsis Genome |
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Authors: | David Benovoy Guy Drouin |
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Institution: | (1) Département de biologie and Centre de recherche avancée en génomique environnementale, Université d’Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada |
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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.
Electronic Supplementary Material Electronic Supplementary material is available for this article at
and accessible for authorised users.
Reviewing Editor: Dr. Juergen Brosius] |
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Keywords: | Processed pseudogenes Processed genes Spontaneous mutations Arabidopsis thaliana Substitutions |
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